Opinion for the court filed by Circuit Judge BUCKLEY.
Concurring opinion filed by Circuit Judge HENDERSON.
BUCKLEY, Circuit Judge:Sister Elizabeth McDonough and the Equal Employment Opportunity Commission allege that The Catholic University of America engaged in sex discrimination and retaliatory conduct, in violation of Title VII of the Civil Rights Act of 1964, when it denied her application for tenure in its Department of Canon Law. District Judge Louis F. Ober-dorfer dismissed the action as precluded by the First Amendment’s religion clauses. We agree with Judge Oberdorfer that the Free Exercise Clause forbids judicial review of this ease because Sister McDonough’s role at Catholic University was “the functional equivalent of a minister.” We also agree that the application of Title VII to her employment requires an intrusion by the Federal Government in religious affairs that is forbidden by the Establishment Clause.
I. . BACKGROUND
A, The Canon Law Department of The Catholic University of America
The Catholic University of America was chartered by Pope Leo XIII in 1887 as a Roman Catholic institution of higher learning. C. Joseph Nuesse, The Catholic University of America: A Centennial History 52-53 (1990). Originally, the University was “strictly a pontifical institution, functioning under the direction of the Holy See.” Granfield v. Catholic University of America, 530 F.2d 1035, 1043 n. 19 (D.C.Cir.1976). Although the University’s by-laws were amended in 1970, giving it greater independence from the Vatican, it remains a “sectarian institution” that is governed by a Board of Trustees consisting of fifteen members of the American Catholic hierarchy (usually bishops) and fifteen laymen. See id. The University’s Departments of Canon Law and Theology (which are departments within its School of Religious Studies) and its School of Philosophy, however, remain under pontifical direction and hold the canonical status of “ecclesiastical faculties.” See Canonical Statutes of the Ecclesiastical Faculties of the Catholic University of America (“Canonical Statutes”), Part I, Sec. 1.
This case concerns the University’s Department of Canon Law (“Department”). Canon law is the “fundamental body of ecclesiastical laws” of the Roman Catholic Church. Canon Law Society of America, Code of Canon Law xvi (1983). It governs the sacramental life of the Church and defines the obligations and rights of the faithful. Id., Books II and IV. The Department’s stated purpose is “to familiarize the student with the entire body of ecclesiastical law, its development and interpretation,” Statutes of the Ecclesiastical Faculty of Canon Law, Part I; it is the only institution in the United States that is empowered by the Vatican to confer ecclesiastical degrees in church law. Affidavit of Sister Elizabeth McDonough (“McDonough Affidavit”) at ¶ 13, reprinted in Joint Appendix (“JA,.”) 328.
B. Sister Elizabeth McDonough
Sister Elizabeth McDonough is a nun in the Dominican Order. Following her profession of vows, Sister McDonough was assigned to teach mathematics, science, and religion at Catholic high schools in Connecticut and Ohio. In January 1976, her superior suggested that she pursue a degree in canon law, a field of study that the Catholic Church *458had recently opened to women. Accordingly, in the fall of 1978, Sister McDonough enrolled in the School of Religious Studies at Catholic University. In 1979, she transferred to the school’s Department of Canon Law and, in May 1982, became the fifth woman at Catholic University to receive a Doctorate of Canon Law.
Soon after receiving her degree, Sister McDonough applied for a teaching position in the Department. Her application was accepted and, in 1983, she became the first woman to be admitted to its faculty with a tenure track appointment. In addition to teaching classes, Sister McDonough assisted students, published articles, and performed various consulting services. In 1988, she was promoted to the rank of associate professor and began inquiring into her prospects for securing tenure.
C. Tenure Application within the Department of Canon Law
In order to secure tenure in the Department of Canon Law, an applicant’s qualifications must first be reviewed by three academic bodies: the tenured faculty members within the Department, the School of Religious Studies’ Committee on Appointments and Promotions (“School CAP”), and the Academic Senate’s Committee on Appointments and Promotions (“Senate CAP”). A favorable recommendation by any of these bodies requires the vote of a majority of those participating in the consideration of a case. The procedures governing these reviews are set forth in the University’s Faculty Handbook and are generally applicable to all candidates for tenured positions at the University. Because the Department of Canon Law is an ecclesiastical faculty, however, an applicant for tenure in the Department who has survived the review of his academic peers must also be approved by ecclesiastical authorities in accordance with the procedures set forth in the University’s Canonical Statutes. Affidavit of Father James H. Provost (“Provost Affidavit”) at 6, reprinted in J.A. 478. These provide that, after the candidate has received the affirmative recommendation of the Senate CAP, the President of the University must forward to the Chancellor, who is, ex officio, the Archbishop of Washington, the application and all relevant information regarding the appropriateness of the candidate’s appointment to an ecclesiastical faculty. Canonical Statutes, Part III, Sec. 6, Part V, Sec. 3. It is the Chancellor who “grants the canonical mission to teach in the name of the Church.” Id., Part V, Sec. 4.
The Canonical Statutes provide, further, that before the Chancellor may appoint a person to a tenured professorship, the members of the Board of Trustees who are bishops must review the application and, after consultation with the Vatican, make “a declaration to the Chancellor that there is no impediment to the appointment.” Id., Part V, Sec. 6.1 & n. 3 (noting “existence of an agreement between the Chancellor and the Apostolic See regarding consultation of the Apostolic See prior to the making of this declaration by the episcopal members of the Board”). In the case of one of the Department’s tenured professors, the process of consultation extended over a period of seventeen months, in which he responded in writing to questions presented by the Vatican through the Archbishop of Washington and met with several groups of bishops, cardinals, and other church officials both in the United States and in Rome. Provost Affidavit at 7, J.A. 479.
Sister McDonough submitted her initial tenure application in August 1988. On October 4, 1988, the Canon Law Faculty voted not to recommend tenure by a “split negative vote” of two in favor, three against, and one abstention. She appealed this decision to the School CAP which, without voting, returned her application to the Department for reconsideration in light of a new article she had published. On November 15, 1988, the Canon Law Faculty held a second vote and again faded to muster the majority required to endorse her application. After consulting with members of her religious congregation, Sister McDonough withdrew her application.
Sister McDonough submitted a revised application the following January; and, for the third time, the Canon Law Faculty withheld an affirmative recommendation by a vote of three to three. She again appealed to the School CAP, which this time voted in favor of *459tenure and forwarded her application to the next level of review, the Senate CAP. This body denied Sister McDonough the absolute majority required for a recommendation by a vote of three in favor, one against, and two abstentions.
Sister McDonough appealed the Senate CAP’s decision, alleging that she had received “differential and unfair treatment.” McDonough Affidavit at ¶ 107, J.A. 375. The University’s Academic Vice President granted her appeal and returned the application to the Senate CAP for reconsideration, citing “substantive and procedural questions.” During the interval between the Senate CAP’s initial vote and its reconsideration of her application, Sister McDonough submitted copies of a new article that she had published; and the University asked certain external evaluators to comment on her scholarship. Sister McDonough also wrote letters to two members of the Senate CAP expressing her belief that she was being held to a higher standard because of her sex. On November 14, 1989, after reviewing the new publication and despite the favorable tenor of the external evaluations, the Senate CAP voted unanimously not to recommend tenure. The reasons given for the denial were:
1. The scholarship of the candidate does not measure up to the standards expected in the field for the granting of tenure;
2. While the committee recognized the candidate’s contribution to service and the practice of canon law, in its opinion this factor does not counterbalance the marginal performance in teaching and scholarly publications;
3. Considering the split vote of the departmental faculty and the Committee on Appointments and Promotions of the School of Religious Studies, the committee could not “be assured beyond reasonable doubt that the candidate under review possesses ... the optimal qualifications for the position” and therefore is constrained to “recommend against the granting of tenure” (Faculty Manual, p. 8).
EEOC v. Catholic University of America, 856 F.Supp. 1, 8 (D.D.C.1994) (“Catholic University ”) (quoting memorandum dated Nov. 15, 1989, fi"om Professor Virgil Nem-oianu to Academic Vice President John Wip-pel). Sister McDonough’s employment as an associate professor with the Department of Canon Law expired on August 31,1990.
D. The EEOC and the District Court Proceedings
Sister McDonough filed discrimination charges against Catholic University with the Equal Employment Opportunity Commission on January 18,1990. After a two-year investigation and failed efforts at conciliation, the EEOC joined Sister McDonough in instituting this action in which they allege that, in denying Sister McDonough’s application for tenure, Catholic University engaged in sex discrimination and retaliatory conduct in violation of Title VII of the Civil Rights Act of 1964,42 U.S.C. § 2000e et seq.
The case went to trial on November 3, 1993, and was concluded one week later. What emerged as the critical factual issue was whether the University’s stated reasons for denying tenure, namely, Sister McDon-ough’s “marginal performance in teaching and scholarly publications,” were pretextual. In order to establish that they were, Sister McDonough introduced testimony comparing her performance with that of the two most recent applicants to be granted tenure in the Department of Canon Law, both of whom were men. This comparison largely focused on the quantity of her publications and the quality of her scholarship as reflected in them.
During the presentation of evidence, Judge Oberdorfer expressed his uneasiness at “sitting on the qualifications of an expert in canon law” and suggested that the line of inquiry was “getting awful[ly] close to entangling the government and the judiciary in religious matters.” Nov. 4, 1993 Trial Transcript at 9-10, J.A. 199. See also Nov. 5, 1993 Trial Transcript at 147, J.A. 240 (“I’ve got to pass on people’s judgment about colleagues in a religious setting ... and when I hear this ... aggressive examination of a priest about what is at least partly his clerical duties, I’ve got a problem.”). Shortly thereafter, he asked the parties to submit briefs on whether he had the constitutional authority to hear the case.
*460After reviewing the parties’ submissions and hearing oral argument, Judge Oberdor-fer dismissed the case without reaching the merits. He concluded that the “application of Title VII to [the facts and relationships] would violate both the Free Exercise and the Establishment Clauses_” Catholic University, 856 F.Supp. at 9. Specifically, he found that “Sister McDonough’s primary role in the Department of Canon Law was the functional equivalent of the task of a minister,” id. at 10, and concluded that “the Free Exercise Clause precludes review of this employment decision.” Id. at 11. He also held that the Establishment Clause barred adjudication of Sister McDonough’s claims on the ground that “[a] judicial evaluation of the ‘quality’ of [her] canon law scholarship would constitute^] and the prolonged monitoring and investigation by the EEOC has constituted^] excessive entanglement with reli-gion_” Mat 12.
In their appeal from the district court’s order, appellants make a number of arguments, of which the following warrant analysis: (1) the “ministerial exception” relied on by the district court has been discredited by the Supreme Court’s decision in Employment Division, Dep’t of Human Resources of Oregon v. Smith, 494 U.S. 872, 110 S.Ct. 1595, 108 L.Ed.2d 876 (1990); (2) even if the exception remains valid, it does not apply to the facts of this case; and (3) because the district court was not required to address any religious issues, the case could not have posed a risk of “undue governmental entanglement” with religion in violation of the Establishment Clause.
II. Analysis
This case presents a collision between two interests of the highest order: the Government’s interest in eradicating discrimination in employment and the constitutional right of a church to manage its own affairs free from governmental interference. As in many cases dealing with the autonomy of religious bodies, this one requires analysis under both the Free Exercise and Establishment Clauses of the First Amendment. We address each in turn.
A. The Free Exercise Clause
The Free Exercise Clause provides that “Congress shall make no law ... prohibiting the free exercise [of religion].” U.S. Const, amend. I. The limits placed by the First Amendment on the Government extend to its judicial as well as legislative branch. See Kreshik v. Saint Nicholas Cathedral of the Russian Orthodox Church of North America, 363 U.S. 190, 191, 80 S.Ct. 1037, 1038, 4 L.Ed.2d 1140 (1960).
The Supreme Court has recognized that government action may burden the free exercise of religion, in violation of the First Amendment, in two quite different ways: by interfering with a believer’s ability to observe the commands or practices of his faith, see, e.g., Church of the Lukumi Babalu Aye, Inc. v. City of Hialeah, 508 U.S. 520, 531-33, 113 S.Ct. 2217, 2226, 124 L.Ed.2d 472 (1993) (“the protections of the Free Exercise Clause pertain if the law at issue discriminates against some or all religious beliefs or regulates or prohibits conduct because it is undertaken for religious reasons”), and by encroaching on the ability of a church to manage its internal affairs. See, e.g., Kedroff v. St. Nicholas Cathedral of the Russian Orthodox Church in North America, 344 U.S. 94, 116, 73 S.Ct. 143, 154-55, 97 L.Ed. 120 (1952) (Free Exercise Clause protects power of religious organizations “to decide for themselves, free from state interference, matters of church government as well as those of faith and doctrine”).
The Supreme Court has shown a particular reluctance to interfere with a church’s selection of its own clergy. See, e.g., Gonzalez v. Roman Catholic Archbishop of Manila, 280 U.S. 1, 16, 50 S.Ct. 5, 7-8, 74 L.Ed. 131 (1929) (“it is the function of the church authorities to determine what the essential qualifications of a chaplain are and whether the candidate possesses them”); Serbian Eastern Orthodox Diocese v. Milivojevich, 426 U.S. 696, 717, 96 S.Ct. 2372, 2384, 49 L.Ed.2d 151 (1976) (“questions of church discipline and the composition of the church hierarchy are at the core of ecclesiastical concern”).
*461 1. The Ministerial Exception
Relying on these and other eases, this circuit and a number of others have long held that the Free Exercise Clause exempts the selection of clergy from Title VII and similar statutes and, as a consequence, precludes civil courts from adjudicating employment discrimination suits by ministers against the church or religious institution employing them. See, e.g., Minker v. Baltimore Annual Conference of the United Methodist Church, 894 F.2d 1354, 1358 (D.C.Cir.1990) (adjudication of minister’s Age Discrimination in Employment Act claim against his church would violate' the Free Exercise Clause); McClure v. Salvation Army, 460 F.2d 553, 558, 560 (5th Cir.1972) (recognizing that “[t]he relationship between an organized church and its ministers is its lifeblood” and that application of Title VII to this relationship would encroach on religious freedom); Young v. Northern Illinois Conference of United Methodist Church, 21 F.3d 184 (7th Cir.1994) (Free Exercise Clause bars Title VII action by probationary minister against her church); Scharon v. St. Luke’s Episcopal Presbyterian Hospitals, 929 F.2d 360 (8th Cir.1991) (religion clauses bar application of Title VII and Age Discrimination in Employment Act claims of chaplain against church-affiliated hospital); Natal v. Christian and Missionary Alliance, 878 F.2d 1575 (1st Cir.1989) (Free Exercise Clause bars wrongful termination action brought by clergyman against not-for-profit religious corporation). We have noted that in excepting the employment of a minister from Title VII, “[w]e need not find that the factors relied upon by [a] Church [are] independently ecclesiastical in nature, only that they [are] related to a pastoral appointment determination.” Minker, 894 F.2d at 1357 (citing Granfield, 530 F.2d at 1047 (salary of priests an internal religious question)).
The ministerial exception has not been limited to members of the clergy. It has also been applied to lay employees of religious institutions whose “primary duties consist of teaching, spreading the faith, church governance, supervision of a religious order, or supervision or participation in religious ritual and worship_” Rayburn v. General Conference of Seventh-day Adventists, 772 F.2d 1164, 1169 (4th Cir.1985) (internal quotation marks and citation omitted). If their positions are “important to the spiritual and pastoral mission of the church,” they “should be considered ‘clergy.’ ” Id. See also Scharon, 929 F.2d at 362-63 (position of hospital chaplain is “primarily a ‘ministerial’ position”); EEOC v. Southwestern Baptist Theological Seminary, 651 F.2d 277, 283 (5th Cir.1981) (for purposes of exception, “ministers” includes non-ordained faculty at Baptist seminary where no course has “a strictly secular purpose”); Powell v. Stafford, 859 F.Supp. 1843, 1346-47 (D.Colo.1994) (theology teacher at Catholic high school). In this case, the district court found that Sister McDonough’s employment met this “ministerial function” test. Catholic University, 856 F.Supp. at 10-11.
2. Did the Ministerial Exception Survive Smith?
Appellants argue that the district court erred in dismissing this case under the ministerial exception because, in their view, that exception did not survive the Supreme Court’s decision in Employment Division, Dep’t of Human Resources of Oregon v. Smith, 494 U.S. 872, 110 S.Ct. 1595, 108 L.Ed.2d 876 (1990). In Smith, the Supreme Court addressed the issue of “whether the Free Exercise Clause ... permitted] the State of Oregon to include religiously inspired peyote use within the reach of its general- criminal prohibition on use of that drug.” Id. at 874, 110 S.Ct. at 1597. In holding that the Clause did not require Oregon to permit the religious use of peyote, the Court explained that
the right of free exercise does not relieve an individual of the obligation to comply with a valid and neutral law of general applicability on the ground that the law proscribes ... conduct that his religion prescribes....
Id. at 879, 110 S.Ct. at 1600 (internal quotation marks omitted).
Relying on this language, appellants argue that because Title VII is a religion-neutral law of general applicability, the Free Exercise Clause does not bar its application to *462ministers employed by religious organizations. They assert that the ministerial exception was based on a test applied in Free Exercise Clause cases before Smith that required the Government to demonstrate the existence of a compelling governmental interest that would justify the burden placed on the right of free exercise by a particular statute. They then argue that Smith rejected the compelling interest test in the case of religion-neutral laws of general application with the result that the ministerial exception has been stripped of its constitutional foundation. Catholic University does not challenge this reasoning; rather, it replies that the compelling interest test has been reinstated by the Religious Freedom Restoration Act of 1993, which was enacted by Congress in response to Smith. For her part, Sister McDonough challenges both the constitutionality of that act and its retroactive application to this case.
Whatever the constitutionality and effect of this statute, which we will address later, we disagree with appellants’ conclusion that Smith requires the rejection of the ministerial exception. We acknowledge that the Court stated that it has “never held that an individual’s religious beliefs excuse him from compliance with an otherwise valid law prohibiting conduct that the State is free to regulate,” id. at 878-79, 110 S.Ct. at 1600 (emphasis added), and that it has
consistently held that the right of free exercise does not relieve an individual of the obligation to comply with a valid and neutral law of general applicability on the ground that the law proscribes (or prescribes) conduct that his religion prescribes (or proscribes).
Id. at 879, 110 S.Ct. at 1600 (internal quotation marks and citation omitted) (emphasis added). It does not follow, however, that Smith stands for the proposition that a church may never be relieved from such an obligation. We say this for two reasons. First, the burden on free exercise that is addressed by the ministerial exception is of a fundamentally different character from that at issue in Smith and in the cases cited by the Court in support of its holding. The ministerial exception is not invoked to protect the freedom of an individual to observe a particular command or practice of his church. Rather, it is designed to protect the freedom of the church to select those who will carry out its religious mission. Moreover, the ministerial exception does not present the dangers warned of in Smith. Protecting the authority of a church to select its own ministers free of government interference does not empower a member of that church, “by virtue of his beliefs, ‘to become a law unto himself.’” Id. at 885, 110 S.Ct. at 1603 (quoting Reynolds v. United States, 98 U.S. 145, 167, 25 L.Ed. 244 (1879)). Nor does the exception require “judges to determine the ‘centrality1 of religious beliefs before applying a ‘compelling interest’ test in the free exercise field.” Id. at 887, 110 S.Ct. at 1604.
Second, while it is true that some of the cases that have invoked the ministerial exception have cited the compelling interest test, e.g., McClure, 460 F.2d at 558, all of them rely on a long line of Supreme Court cases that affirm the fundamental right of churches to “decide for themselves, free from state interference, matters of church government as well as those of faith and doctrine.” Kedroff, 344 U.S. at 116, 73 S.Ct. at 154. See, e.g., Watson v. Jones, 80 U.S. (18 Wall.) 679, 727, 20 L.Ed. 666 (1871) (“questions of discipline, or of faith, or ecclesiastical rule, custom, or law [that] have been decided by the highest of .. church judicatories ... must [be] accepted] ... as final”); Gonzalez, 280 U.S. at 16, 50 S.Ct. at 7 (“it is the function of the church authorities to determine what the essential qualifications of a chaplain are”); Kedroff, 344 U.S. at 107-08, 73 S.Ct. at 150 (“Legislation that regulates church administration, the operation of the churches, the appointment of clergy ... prohibits the free exercise of religion.”); Walz v. Tax Commission of the City of New York, 397 U.S. 664, 672, 90 S.Ct. 1409, 1413, 25 L.Ed.2d 697 (1970) (“we have been able to chart a course that preserved the autonomy and freedom of religious bodies”).
We agree with the Fifth Circuit that “throughout these opinions there exists a spirit of freedom for religious organizations, an independence from secular control or ma-nipulation_” McClure, 460 F.2d at 560 *463(internal quotation marks omitted). We have considered the autonomy of a religious body in the selection and training of its own clergy to be of critical importance. Thus, in Mink-er, we stated that “[w]e cannot imagine an area of inquiry less suited to a temporal court for decision; evaluation of the ‘gifts and graces’ of a minister must be left to ecclesiastical institutions.” 894 F.2d at 1357. We also reaffirmed that “[t]he Free Exercise Clause precludes governmental interference with ecclesiastical hierarchies, church administration, and appointment of clergy.” Id. (quoting King’s Garden, Inc. v. FCC, 498 F.2d 51, 56 (D.C.Cir.1974)) (emphasis added).
We acknowledge that Kedroff and the other Supreme Court eases that we and other courts have cited in support of the ministerial exception did not involve neutral statutes of general application. Nevertheless, we cannot believe that the Supreme Court in Smith intended to qualify this century-old affirmation of a church’s sovereignty over its own affairs. See Douglas Laycock, Towards a General Theory of the Religion Clauses: The Case of Church Labor Relations and the Right to Church Autonomy, 81 Colum.L.Rev. 1373, 1397 (1981) (noting that the Supreme Court has been willing to extend the “right of church autonomy as far as necessary to include the cases before it.”).
We conclude from our review of the Supreme Court’s First Amendment jurisprudence that whereas the Free Exercise Clause guarantees a church’s freedom to decide how it will govern itself, what it will teach, and to whom it will entrust its ministerial responsibilities, it does not guarantee the right of its members to practice what their church may preach if that practice is forbidden by a neutral law of general application. But even if we misread Smith, our finding that the application of Title VII would violate the Free Exercise Clause nevertheless survives under an exception to the general rule in Smith that we discuss below at the conclusion of our Establishment Clause analysis.
3. Does the Ministerial Exception Apply to Sister McDonough ?
Sister McDonough argues that even if the ministerial exception is still valid, the district court applied it too broadly in this ease. She emphasizes the fact that she is not an ordained minister and argues that her duties were not pervasively religious. We find her first assertion immaterial and disagree with the second.
In Minker, the only previous case in which we applied the ministerial exception, the plaintiff was an ordained minister. Accordingly, we had no need to determine whether the exception should extend to persons who, though not ordained, nevertheless performed “ministerial functions.” 894 F.2d at 1358. As stated earlier, however, other courts have extended the exception to include employees of religious institutions whose duties are religious in nature. See, e.g., Rayburn, 772 F.2d at 1165 (associate pastor who had completed seminary training but was not ordained, and whose role involved preaching and other “evangelical, liturgical, and coun-selling responsibilities”); Southwestern Baptist, 651 F.2d at 280, 283 (seminary faculty who instructed seminarians in the “whole of religious doctrine,” were predominantly ordained ministers, and were evaluated primarily on their “Christian character, positive and consecrated attitudes, [and] faithful allegiance to the Baptist faith” and only secondarily on their scholastic attainments). We find their logic persuasive and agree that the ministerial exception encompasses all employees of a religious institution, whether ordained or not, whose primary functions serve its spiritual and pastoral mission. See Rayburn, 772 F.2d at 1169.
We therefore consider whether Sister Mc-Donough’s responsibilities as a member of the Canon Law Faculty would be essentially religious. In making this determination, we ask whether her “primary duties [would] consist of teaching, spreading the faith, church governance, supervision of a religious order, or supervision or participation in religious ritual and worship.” Id. (quoting B. Bagni, Discrimination in the Name of the Lord: A Critical Evaluation of Discrimination by Religious Organizations, 79 Colum.L.Rev. 1514,1545 (1979)). Sister McDonough clearly fits this description. She would be a member of an ecclesiastical faculty whose stated mission is to “foster and teach sacred *464doctrine and the disciplines related to it.” Canonical Statutes of the Ecclesiastical Faculties of The Catholic University of America (“Canonical Statutes”), Part I, Sec. 2. See also id., Part II, See. 3(c) (purposes of the ecclesiastical faculties include the instruction of students in “ministerial studies”). The courses taught by the Canon Law Faculty are designed
to prepare the student for the professional practice of canon law — in diocesan and religious curias and in ecclesiastical tribunals — for the teaching of canon law, and for scientific canonical research.
Statutes of the Ecclesiastical Faculty of Canon Law, Part I. As a member of that faculty, she would be entrusted with instructing students in the “fundamental body of ecclesiastical laws” that governs the Church’s sacramental life, defines the rights and duties of its faithful and the responsibilities of their pastors, and guides its administration. See Code of Canon Law, xxix-xlii (“Outline of the Code by Canons”).
We find, moreover, that the role performed by the faculty is vital to the spiritual and pastoral mission of the Catholic Church. The Department is the sole entity in the United States empowered by the Vatican to confer ecclesiastical degrees in canon law. To this end, the University requires that the courses and programs of the Department “be conducted according to norms and regulations promulgated by the Holy See.” Special Statutes for Pontifical Schools, Part II, Faculty Handbook of The Catholic University of America (“Faculty Handbook”) at 25. Thus the University’s ecclesiastical faculties serve as the instruments established by the Catholic Church in the United States for teaching its doctrines and disciplines.
It is important to note in this respect the role that the Canon Law Faculty plays in the graduate education of American priests. Although members of the laity have recently been allowed to enroll in the Department, over 95 percent of the students in the Department between 1983 and 1993 were ordained or members of a religious order. Catholic University, 856 F.Supp. at 4. In those same years, 26 of the 37 Doctorates of Canon Law awarded by the Department went to priests; of the remaining eleven degrees, eight were awarded to members of religious orders and only three to laymen. Id. In short, members of the Canon Law Faculty perform the vital function of instructing those who will in turn interpret, implement, and teach the law governing the Roman Catholic Church and the administration of its sacraments. Although Sister Mc-Donough is not a priest, she is a member of a religious order who sought a tenured professorship in a field that is of fundamental importance to the spiritual mission of her Church. That the Canonical Statutes reserve in the Vatican a veto over appointments to tenured positions in the Canon Law Faculty (see p. 4-5 supra) confirms our understanding of their pastoral and spiritual significance. Cf. concurring opinion at 475-76.
In light of the foregoing, we reject Sister McDonough’s attempt to liken her situation to those of the plaintiffs in cases such as Weissman v. Congregation Shaare Emeth, 38 F.3d 1038 (8th Cir.1994); Geary v. Visitation of the Blessed Virgin Mary Parish School, 7 F.3d 324 (3d Cir.1993); and De-Marco v. Holy Cross High School, 4 F.3d 166 (2d Cir.1993), in which the First Amendment was not found to bar the adjudication of employment discrimination claims. Those cases are readily distinguished because the functions performed by the plaintiffs were not ministerial. For example, in Weissman, the plaintiff was able to bring an age discrimination action against his temple without violating the First Amendment because
Weissman was responsible for logistical support of activities including supervision of administrative, clerical, building maintenance, and custodial personnel. He also managed property and equipment and maintained financial records. He was not a member of the clergy and played no role in decisions relating to spiritual matters.
38 F.3d at 1040. See also Geary, 7 F.3d at 331 (lay teacher in elementary parochial school); DeMarco, 4 F.3d at 171-72 (lay math teacher).
That the University did not assert any religious basis for denying Sister McDon-ough tenure does not affect our conclusion; *465nor does the fact that her application never reached the ecclesiastical levels of review. The focus under the ministerial exception is on the action taken, not possible motives:
[T]he free exercise clause of the First Amendment protects the act of a decision rather than a motivation behind it. In these sensitive areas, the state may no more require a minimum basis in doctrinal reasoning than it may supervise doctrinal content.
Rayburn, 772 F.2d at 1169. As we noted in Minker, “[w]e need not find that the factors relied upon by the Church were independently ecclesiastical in nature, only that they were related to a pastoral appointment determination.” 894 F.2d at 1357.
Because Sister McDonough’s employment as a tenured member of the Department of Canon Law so clearly meets the ministerial function test, we affirm the district court’s dismissal of Sister McDonough’s claims on the basis of the Free Exercise Clause.
B. The Establishment Clause
The Establishment Clause provides that “Congress shall make no law respecting an establishment of religion-” U.S. Const. amend. I. In Lemon v. Kurtzman, 403 U.S. 602, 91 S.Ct. 2105, 29 L.Ed.2d 745 (1971), the Supreme Court established a three-part test for determining whether a statute violates the Establishment Clause:
First, the statute must have a secular legislative purpose; second, its principal or primary effect must be one that neither advances nor inhibits religion; finally, the statute must not foster an excessive government entanglement with religion.
Id. at 612-13, 91 S.Ct. at 2111 (citation and internal quotation marks omitted).
The district court concluded that
[t]he monitoring of and investigation into the tenure decisions of the Canon Law Department by the EEOC and the courts, and the possible judicial involvement in a larger doctrinal intra-church controversy, has impermissibly entangled the civil authorities in religious decision-making, and would do so in the future.
Catholic University, 856 F.Supp. at 13. Although it is difficult to attach a precise meaning to the word “entanglement,” courts have found an unconstitutional entanglement with religion in situations where a “protracted legal process pit[s] church and state as adversaries,” Rayburn, 772 F.2d at 1171, and where the Government is placed in a position of choosing among “competing religious visions.” Geary, 7 F.3d at 330. In this case, the court found that the controversy over Sister McDonough’s qualifications for tenure placed it in the impermissible position of having “to evaluate ... competing opinions on religious subjects,” and that the EEOC’s “prolonged monitoring and investigation” violated the Establishment Clause. Catholic University, 856 F.Supp. at 9, 12.
1. Assessing Sister McDonough’s Qualifications to be a Tenured Professor of Canon Law
Catholic University asserted that it had denied Sister McDonough’s application because her teaching and scholarship failed to meet the standards required of a tenured member of the Canon Law Faculty. The central issue at trial was whether those reasons were pretextual. The parties introduced an extensive body of conflicting testimony concerning the quality of Sister Mc-Donough’s publications, which she concedes “were of a religious nature.” Reply Brief for Appellant McDonough at 18. Of the eighteen witnesses called to testify concerning her qualifications, fourteen were clergy or members of a religious order.
In dismissing the action on Establishment Clause grounds, the district court explained:
[A] trier of fact chooses between competing expert opinions. There are such competing expert opinions as to the quality and, necessarily, the religious substance of Sister McDonough’s writings in this record. I find and conclude that it is neither reasonably possible nor legally permissible for a lay trier of faet to evaluate these competing opinions on religious subjects.
Catholic University, 856 F.Supp. at 9. The EEOC nevertheless insists, based on Jones v. Wolf, 443 U.S. 595, 99 S.Ct. 3020, 61 L.Ed.2d 775 (1979), that this dispute can be *466resolved without entangling the Government “in questions of religious doctrine, polity, and practice” by invoking “neutral principles of law” that “rel[y] on objective, well established concepts of ... law familiar to lawyers and judges.” Brief for Appellant EEOC at 23 (quoting Jones, 443 U.S. at 603, 99 S.Ct. at 3025). Jones, however, dealt with a dispute over church property, and the “neutral principles” to which the Supreme Court referred were those embodied in trust and property law. As we pointed out in Minker, the neutral principles test adopted in Jones will only “permit[ ] a court to interpret provisions of religious documents involving ... non-doctrinal matters as long as the analysis can be done in purely secular terms.” 894 F.2d at 1358 (emphasis added).
Although an assessment of scholarship undoubtedly involves objective criteria that are independent of religious content, the clergy and members of religious orders who were asked to evaluate Sister McDonough’s publications could not escape the knowledge that they were being asked to determine whether she was qualified for a position in which she would “teach in the name of the Church.” Canonical Statutes, Part V, Sec. 4. Under the circumstances, there was the inevitable risk that the persons assessing the scholarship of a particular paper would consider whether her conclusions were in accord with what the Church teaches or what, in their judgment, the Church ought to teach.
Judge Oberdorfer attempted to decide the case in accordance with neutral principles; but after a week of trial, he found that “no expert testimony c[ould] effectively filter out the religious elements from the secular ones sufficiently to avoid unwholesome and impermissible entanglement with religious concerns.” Catholic University, 856 F.Supp. at 12. That a judge of his experience should have reached this conclusion is perhaps the best evidence that the pretext inquiry would have required him “to choose between [the witnesses’] competing religious visions.” Geary, 7 F.3d at 330.
Finally, while it is true that the Senate CAP was a secular body and that it examined her qualifications in accordance with the secular criteria set forth in the Faculty Handbook, see concurring opinion at 471-72, it is by no means clear that its decision was unaffected by religious considerations. In reviewing Sister McDonough’s credentials, the Senate CAP was required to consider, among other factors, “[t]he purpose of [her] appointment ... in relation to the mission and needs of the [Canon Law] Department.” Faculty Handbook, Part II, Art. 13. The mission of that Department, of course, is religious; and we cannot determine the degree, if any, to which that body was influenced by the votes against tenure that had been cast by members of the Canon Law Faculty, all of whom were priests who may have questioned Sister McDonough’s qualifications on religious grounds. What the record does reveal is that the Senate CAP declined to recommend tenure in part because some members of the departmental faculty had opposed her candidacy. See p. 6 supra.
In light of the above, we agree with Judge Oberdorfer that “[e]ivil courts should not be entangled in such disputes.” Catholic University, 856 F.Supp. at 12.
2. The EEOC’s Investigation and Litigation
As the Supreme Court has observed, “[i]t is not only the conclusions that may be reached by [an agency] which may impinge on rights guaranteed by the Religion Clauses, but also the very process of inquiry leading to findings and conclusions.” NLRB v. Catholic Bishop of Chicago, 440 U.S. 490, 502, 99 S.Ct. 1313, 1320, 59 L.Ed.2d 533 (1979). Cf. Aguilar v. Felton, 473 U.S. 402, 413, 105 S.Ct. 3232, 3238, 87 L.Ed.2d 290 (1985) (“pervasive monitoring by public authorities in the sectarian schools infringes precisely on those Establishment Clause values at the root of the prohibition of excessive entanglement.”).
An excessive entanglement may occur where there is a sufficiently intrusive investigation by a government entity into a church’s employment of its clergy. In Young, for example, the Seventh Circuit stated that “civil court review of ecclesiastical decisions ...[,] particularly those pertaining to the hiring or firing of clergy, are in themselves an ‘extensive inquiry into religious law and *467practice, and hence forbidden by the First Amendment.” 21 F.3d at 187 (construing Milivojevich, 426 U.S. 696, 96 S.Ct. 2372) (emphasis in original). Although we did not address the Establishment Clause in Minker, we nevertheless observed that “any inquiry into the Church’s reasons for asserting that Minker was not suited for a particular pas-torship would constitute an excessive entanglement in its affairs.” 894 F.2d at 1360.
In this ease, the EEOC’s two-year investigation of Sister McDonough’s claim, together with the extensive pre-trial inquiries and the trial itself, constituted an impermissible entanglement with judgments that fell within the exclusive province of the Department of Canon Law as a pontifical institution. See Rayburn, 772 F.2d at 1171 (noting that a Title VII action is a “potentially ... lengthy proceeding” that could subject church personnel and records to subpoena, discovery, and cross-examination). This suit and the extended investigation that preceded it has caused a significant diversion of the Department’s time and resources. Moreover, we think it fair to say that the prospect of future investigations and litigation would inevitably affect to some degree the criteria by which future vacancies in the ecclesiastical faculties would be filled. Having once been deposed, interrogated, and haled into court, members of the Department of Canon Law and of the faculty review committees who are responsible for recommending candidates for tenure would do so “with an eye to avoiding litigation or bureaucratic entanglement rather than upon the basis of their own personal and doctrinal assessments of who would best serve the ... needs” of the Department. Id.
These conclusions are a sufficient basis for affirming the district court’s dismissal of this case under the Establishment Clause. We think it worth noting, nevertheless, that those conclusions also bring this case within an exception to the rule in Smith that the right of free exercise is not a defense against the application of a neutral law of general application, such as Title VII. There, the Court specifically identified a class of cases in which it held “that the First Amendment bars application of a neutral, generally applicable law.” Smith, 494 U.S. at 881, 110 S.Ct. at 1601. These cases have involved not the Free Exercise Clause alone, but the Free Exercise Clause in conjunction with other constitutional protections....” Id. Among the examples cited by the Court are Cantwell v. Connecticut, 310 U.S. 296, 60 S.Ct. 900, 84 L.Ed. 1213 (1940), and Murdock v. Pennsylvania, 319 U.S. 106, 63 S.Ct. 870, 87 L.Ed. 1292 (1943) (combination of free exercise and freedom of speech concerns), and Wisconsin v. Yoder, 406 U.S. 205, 92 S.Ct. 1526, 32 L.Ed.2d 15 (1972) (combining free exercise concerns with the right of parents to direct the education of their children). Smith, 494 U.S. at 881, 110 S.Ct. at 1601. We have demonstrated that the EEOC’s attempt to enforce Title VII would both burden Catholic University’s right of free exercise and excessively entangle the Government in religion. As a consequence, this case presents the kind of “hybrid situation” referred to in Smith that permits us to find a violation of the Free Exercise Clause even if our earlier conclusion that the ministerial exception survived Smith should prove mistaken.
C. The Religious Freedom Restoration Act
The ministerial exception is judicial shorthand for two conclusions: the first is that the imposition of secular standards on a church’s employment of its ministers will burden the free exercise of religion; the second, that the state’s interest in eliminating employment discrimination is outweighed by a church’s constitutional right of autonomy in its own domain. Catholic University argues, essentially, that even if Smith’s rejection of the compelling interest test undermined the exception, the test and the exception were revalidated by the Religious Freedom Restoration Act of 1993, 42 U.S.C. § 2000bb, et seq. (Supp.V.1993) (“RFRA” or “Act”).
If the University is right, it wins the case on this basis alone because we have concluded above that Title VII impermissibly burdens Catholic University’s free exercise of religion and because, in Minker, we made the implicit finding, which we today make explicit, that the Government’s interest in eliminating employment discrimination is insufficient to overcome a religious institution’s interest *468in being able to employ the ministers of its choice. See Minker, 894 F.2d at 1357. Appellants ask us to reject the University’s argument on three grounds: (1) the University has waived the right to invoke RFRA on appeal because it failed to do so before the district court; (2) the Act is unconstitutional; and (3) even if it is constitutional, the Act cannot be applied retroactively.
RFRA provides, in pertinent part:
§ 2000bb. Congressional findings and declaration of purposes
$ ‡ ‡ ‡ ‡
(b) Purposes
The purposes of this chapter are—
(1) to restore the compelling interest test as set forth in Sherbert v. Vemer, 374 U.S. 398 [83 S.Ct. 1790, 10 L.Ed.2d 965] (1963), and Wisconsin v. Yoder, 406 U.S. 205 [92 S.Ct. 1526, 32 L.Ed.2d 15] (1972), and to guarantee its application in all cases where free exercise of religion is substantially burdened; and
(2) to provide a claim or defense to persons whose religious exercise is substantially burdened by government.
§ 2000bb-l. Free exercise of religion protected
(a) In general
Government shall not substantially burden a person’s exercise of religion even if the burden results from a rule of general applicability, except as provided in subsection (b) of this section.
(b) Exception
Government may substantially burden a person’s exercise of religion only if it demonstrates that application of the burden to the person—
(1) is in furtherance of a compelling governmental interest;....
42 U.S.C. §§ 2000bb, 2000bb-l (emphasis added).
Although we remain persuaded that Smith did not affect the ministerial exception, we will now examine appellants’ arguments against our applying RFRA to this case. As a threshold matter, we will dispose of their assertion that RFRA does not have retroactive effect. Although statutes are presumed to apply only prospectively, that presumption does not attach where “Congress has expressly prescribed the statute’s proper reach.” Landgraf v. USI Film Products, — U.S. -, -, 114 S.Ct. 1483, 1505, 128 L.Ed.2d 229 (1994). Here, Congress’s intent could not be clearer. RFRA expressly states that it “applies to all Federal ... law, and the implementation of that law, whether statutory or otherwise, and whether adopted before or after November 16, 1993.” 42 U.S.C. § 2000bb-3(a). See Brown-El v. Harris, 26 F.3d 68, 69 (8th Cir.1994) (“the [RFRA] applies retroactively”). Thus the Act has, in effect, incorporated a statutory “compelling interest” test into Title VII that Catholic University is entitled to invoke if appellants’ other objections are met.
With respect to the argument that Catholic University has waived its right to invoke RFRA, we agree that, as a general rule, we will not consider an argument raised for the first time on appeal. See Singleton v. Wulff, 428 U.S. 106, 120, 96 S.Ct. 2868, 2877, 49 L.Ed.2d 826 (1976). We are not persuaded, however, that Catholic University’s invocation of RFRA raises a “new argument” for purposes of the waiver rule. The gravamen of the University’s argument is not that it is entitled to the statutory defense created by RFRA; rather, it asserts that RFRA has merely restored the pr e-Smith free exercise jurisprudence on which it relied before the district court, including the availability of the compelling interest test. See Brief for Appellee Catholic University at 14 (“[b]ecause RFRA establishes ... heightened protection for the exercise of religion ... [p]roper analysis of the Free Exercise Clause issues involves consideration of the pr e-Smith eases”).
The district court accepted the arguments that Catholic University made on the constitutional issue; namely, that the application of Title VII to the University would violate the Free Exercise Clause on the basis of the ministerial exception as supported by the pre-Smith case law. If we were to conclude that the court came to the right conclusion through erroneous reasoning because it failed to take the effect of Smith’s rejection of the compelling interest test on the exception and the exception’s subsequent restora*469tion by RFRA, we could nonetheless affirm the court by taking account of the Act and its retroactive effect. See Helvering v. Gowran, 302 U.S. 238, 245, 58 S.Ct. 154, 158, 82 L.Ed. 224 (1937) (“if the decision below is correct, it must be affirmed, although the lower court relied upon a wrong ground or gave a wrong reason”); see also Kamen v. Kemper Financial Services, Inc., 500 U.S. 90, 99, 111 S.Ct. 1711, 1718, 114 L.Ed.2d 152 (1991) (“[w]hen an issue ... is properly before the court, the court is not limited to the particular legal theories advanced by the parties, but rather retains the independent power to identify and apply the proper construction of governing law”). The applicability of Title VII to Sister McDonough’s employment is an issue properly before this court. Because taking the Act into account does not require new fact-finding, we will exercise our authority to take cognizance of RFRA as it applies to that issue.
We now reach the question of RFRA’s constitutionality. Sister McDonough argues that the Act is unconstitutional for three reasons: it violates the separation of powers doctrine, Congress lacked the constitutional authority to enact it, and it violates the Establishment Clause. While several commentators have raised significant concern as to the constitutionality of RFRA, see, e.g., Christopher L. Eisgruber & Lawrence G. Sager, Why the Religious Freedom Restoration Act is Unconstitutional, 69 N.Y.U.L.Rev. 437 (1994), the only circuit court of appeals to squarely address the issue has upheld its constitutionality. See Flores v. City of Boerne, Texas, 73 F.3d 1352 (5th Cir.1996); but see Hamilton v. Schriro, 74 F.3d 1545, 1557 (8th Cir.1996) (McMillian, J., dissenting) (concluding that RFRA is unconstitutional).
Before turning to Sister McDonough’s specific challenges, we call attention to two principles that govern the scope of a court’s inquiry into the constitutionality of a federal statute. The first of these is the “principle of the law of federal courts that constitutional issues affecting legislation will not be determined ... in broader terms than are required by the precise facts to which the ruling is to be applied,” Hastings v. Judicial
Conference of the United States, 770 F.2d 1093, 1100 (D.C.Cir.1985) (internal quotations omitted); accordingly, we will limit our inquiry and conclusions to the constitutionality of the Act as it relates to Sister McDonough’s Title VII claim. The second principle requires that a court faced with a challenge to the constitutionality of a federal law “ ‘first ascertain whether a construction of the statute is fairly possible by which the [constitutional] question may be avoided.’ ” United States v. Thirty-Seven Photographs, 402 U.S. 363, 369, 91 S.Ct. 1400, 1404, 28 L.Ed.2d 822 (1971) (quoting Crowell v. Benson, 285 U.S. 22, 62, 52 S.Ct. 285, 296-97, 76 L.Ed. 598 (1932)).
Separation of Powers. Sister Mc-Donough maintains that RFRA violates the separation of powers doctrine by attempting to overturn the Supreme Court’s interpretation of the Free Exercise Clause. She would, of course, be right if that was what the Act purported to do. Although the first paragraph of RFRA’s statement of purposes could be read to support her position, see 42 U.S.C. § 2000bb(b)(l), the presumption of constitutionality and, we believe, the more natural reading of the Act’s provisions lead us to conclude that Congress’s objective in enacting the statute was to overturn the effects of the Smith decision, not the decision itself. The Act does nothing more than substitute a statutory test for the constitutional test that Smith found not to be mandated by the Free Exercise Clause in eases where the right of free exercise was burdened by a neutral law of general application. As the Fifth Circuit observed in Flores, the “RFRA does not usurp the judiciary’s authority to say what the law is any more than did the Voting Rights Act of 1964 when it prohibited literacy tests after Lassiter v. Northampton County Bd. of Elections, 360 U.S. 45, 79 S.Ct. 985, 3 L.Ed.2d 1072 (1959), had upheld their constitutionality.” 73 F.3d at 1363 (citations omitted).
Constitutional Authority. After making the unimpeachable point that Congress may only act pursuant to an enumerated power, Sister McDonough contends that Congress acted beyond its authority in enacting RFRA because “[t]he First Amendment *470of the Constitution does not empower Congress to regulate federal law in order to achieve religious liberty.” Reply Brief for Appellant McDonough at 7. Her argument conflates, however, an enumerated power claim with the quite distinct contention that a given congressional act violates the Establishment Clause. We doubt that she would argue that Congress lacks at least the facial authority to determine against whom, and under what circumstances, Title VII and other federal laws will be enforced. Rather, her complaint is that as a consequence of the enactment of RFRA, those enforcing the laws must now take cognizance of their effect on the free exercise of religion. That question is subsumed in her third challenge, which we now address.
Establishment Clause. Sister McDonough asserts that the Act violates the Establishment Clause by according religion a privileged status. Reply Brief for Appellant Mc-Donough at 6 (citing Board of Education of Kiryas Joel Village School District v. Grumet, — U.S. -, -, 114 S.Ct. 2481, 2491, 129 L.Ed.2d 546 (1994) (Congress violates the Establishment Clause by “prefer[ring] one religion to another, or religion to irreligión”)). But in noting with apparent approval that several States had authorized the sacramental use of peyote, the Court observed, in Smith, that “a society that believes in the negative protection accorded to religious belief can be expected to be solicitous of that value in its legislation as well” and that “to say that a nondiscriminatory religious-practice exemption is permitted ... is not to say that it is constitutionally required. ...” 494 U.S. at 890, 110 S.Ct. at 1606.
Justice O’Connor’s concurring opinion in Corporation of Presiding Bishop of the Church of Jesus Christ of Latterday Saints v. Amos, 483 U.S. 327, 107 S.Ct. 2862, 97 L.Ed.2d 273 (1987), places this matter in the proper perspective. In that opinion, she explained the critical distinction between an “accommodation” and an “endorsement” ■ of religion:
The necessary first step in evaluating an Establishment Clause challenge to a government action lifting from religious organizations a generally applicable regulatory burden is to recognize that such government action does have the effect of advancing religion. The necessary second step is to separate those benefits to religion that constitutionally accommodate the free exercise of religion from those that provide unjustifiable awards of assistance to religious organizations.... [T]he inquiry framed by the Lemon test should be “whether government’s purpose is to endorse religion and whether the statute actually conveys a message of endorsement.”
Id. at 348, 107 S.Ct. at 2874-75 (O’Connor J., concurring), cited with approval in County of Allegheny v. ACLU, Greater Pittsburgh Chapter, 492 U.S. 573, 601 n. 51, 109 S.Ct. 3086, 3105 n. 51, 106 L.Ed.2d 472 (1989). We agree with the Fifth Circuit that RFRA represents nothing more sinister than a “legislatively mandated accommodation of the exercise of religion.” Flores, 73 F.3d at 1364.
In light of the above, we conclude that Congress had the authority, under the Constitution, to create a compelling interest defense for the benefit of those whose free exercise rights would be burdened by a neutral federal law of general application. (As the issue is not before us, we do not decide whether Congress was empowered to include state laws within the reach of the Act. See 42 U.S.C. § 2000bb-3(a) (statute “applies to all Federal and State law”)).
III. Conclusion
For the foregoing reasons, we find that the EEOC’s and Sister McDonough’s claims are barred by the Free Exercise and the Establishment Clauses of the First Amendment and by RFRA The judgment of the district court is therefore
Affirmed.