In an important test of the boundaries of the separation of church and state, the US Supreme Court on Wednesday heard arguments in a case examining whether a parochial school teacher may be barred from filing a discrimination lawsuit against her employer when the suit might entangle government in matters of religious faith.

The high court is being asked to decide whether Cheryl Perich and the Equal Employment Opportunity Commission (EEOC) may sue the Hosanna-Tabor Evangelical Lutheran Church and School in Redford, Mich., for allegedly violating the Americans with Disabilities Act.

The school argues that such a suit is barred under a First Amendment doctrine that recognizes a “ministerial exception” from such litigation because it would require judges to interfere in the pastoral and religious mission of the school.

Lawyers for the EEOC and for the teacher say Ms. Perich was fired in retaliation for filing a discrimination lawsuit against the school. They say there is no “ministerial exception” that would allow religious organizations to fire with impunity an employee whose job primarily involves teaching secular subjects to her students.

The high court has never before identified the contours of the ministerial exception, although such an exception has been recognized and upheld in the lower courts. It has been found to clearly apply to a pastor, priest, or rabbi, but less clear is whether it applies to other employees involved in religious duties.

The Obama administration, arguing on behalf of the EEOC, urged the court to reject the claims of the Lutheran Church and embrace a line of analysis that would have virtually eliminated the ministerial exception.

Some justices shocked

Leondra Kruger, an assistant solicitor general, said the government was basing its argument on a section of the First Amendment that guarantees the freedom of individuals to associate with each other.

Some justices took issue with the position, wondering why the solicitor general’s office wasn’t analyzing the issue through the First Amendment’s religion clauses. The two religion clauses bar the government from establishing a state-favored religion, while prohibiting laws that infringe the free exercise of religion.

The two clauses are widely considered the backbone of religious freedom in the US.

At one point, Justice Elena Kagan asked Ms. Kruger whether she believed that a church has a right grounded in First Amendment religious protections to hire and fire employees without government interference.

Kruger answered that the government was basing its argument on the freedom of association, rather than the parts of the First Amendment that deal with religious freedom.

“We don’t see that line of church autonomy principles in the religion clause jurisprudence as such,” Kruger replied. “We see it as a question of freedom of association.”

The position surprised several justices, including Justice Kagan, the Obama administration’s former solicitor general, who said she found the comment “amazing.” After the hearing, one representative of a religious association called the government’s position a “full frontal assault on religious liberty.”

Chief Justice John Roberts first raised the issue when he asked whether the administration considered anything “special about the fact that the people involved in this case are part of a religious organization.”

Ms. Kruger said, no, that there was no difference whether the group was a religious group, a labor group, or any other association of individuals.

“That’s extraordinary. That is extraordinary,” Justice Antonin Scalia declared. “We are talking here about the free exercise clause and about the establishment clause, and you say they have no special application?”

“We don’t think that the job duties of a particular religious employee are relevant to the inquiry,” she said.

After the argument, Douglas Laycock, a University of Virginia Law School professor who presented the case for the Lutheran church, said he was “encouraged” by the session. He said the justices were “skeptical” of the government’s position.

Mr. Laycock argued that since the teacher in question was the equivalent of a minister and that she taught religious classes to students in addition to secular subjects, the ministerial exception should apply to her case.

Perich also spoke after the argument. “My situation really had nothing to do with religion,” she said.

Perich's story

Perich was employed as one of seven teachers at a K-8 school run by the local Lutheran church. The school had roughly 80 students.

In June 2004, Perich was diagnosed with narcolepsy, a condition in which she would fall into a sudden and deep sleep from which she could not be awakened. She sought treatment.

The school held her job open for a semester by combining classes, but in January 2005 a replacement was hired.

A dispute arose when Perich sought to return to her job in February 2005. The school board said there were no job openings for a teacher. In addition, the board expressed concern about the safety of the children if Perich collapsed while she was supervising them.

Perich threated to sue. The church countered that threatening a lawsuit violated the church’s internal conflict resolution policy. The congregation voted 40 to 11 to fire her.

The EEOC filed a lawsuit on Perich’s behalf charging the church with attempting to retaliate against an employee in violation of the Americans with Disabilities Act. A federal judge sided with the church and threw the suit out, but a panel at the Sixth US Circuit Court of Appeals reversed, ruling that Perich could pursue her lawsuit.

The Sixth Circuit rejected the church’s claim that the suit should be barred by the ministerial exception.

Religious rights vs. rule of law?

During the argument at the high court on Wednesday, several justices expressed concern that Perich’s discrimination suit would excessively entangle the government in an examination of the Lutheran church’s conflict-resolution policy and its desire to have commissioned ministers teaching in Lutheran schools.

Justice Stephen Breyer asked Kruger how the government differentiated between Perich’s Lutheran case and the case of a woman who might sue the Catholic Church for gender discrimination for limiting the priesthood to men.

“The government’s general interest in eradicating discrimination in the workplace is simply not sufficient to justify changing the way that the Catholic Church chooses its priests, based on gender roles that are rooted in religious doctrine,” Kruger said.

“But the interests in this [Lutheran] case are quite different,” she said. “The government has a compelling and indeed overriding interest in ensuring that individuals are not prevented from coming to the government with information about illegal conduct.”

Justice Samuel Alito questioned whether Kruger wasn’t implicitly making a judgment about the relative importance of Catholic versus Lutheran doctrines.

“You think that the Catholic doctrine is older, stronger and entitled to more respect than the Lutheran doctrine,” Justice Alito said.

Kruger disagreed. “The government’s interest in preventing retaliation against those who would go to civil authorities with civil wrongs is foundational to the rule of law,” she said.

The case is Hosanna-Tabor Evangelical Lutheran Church and School v. Equal Employment Opportunity Commission (10-553). A decision is expected by June.