The ministerial exception derives from, and is a specific application of, the long established doctrine of religious autonomy that prohibits or limits civil authorities—including courts—from interfering with matters of religious faith, discipline, internal organization, or ecclesiastical rule, custom or law. It derives from both the Establishment Clause and Free Exercise Clauses of the First Amendment.
The exception applies across statutes, and is not limited to issues of employment of ministers, but extends to the salaries, working conditions, discipline and other matters involved in the relationship between the religious institution and the clergyman.
Despite its name, the ministerial exception is not limited to formal or ordained ministers or to employees with a title of “minister,” but rather applies to all employees whose duties are important to the pastoral mission of the church. It has been applied to teachers in a religious school, even if most of their duties related to secular subjects; to church organists and choir directors; nuns; trainees for the ministry; and similar positions.