The right of Churches in the US to hire and fire their own ministers, is being challenged the US Supreme Court by President Obama’s Equal Employment Opportunity Commission (EEOC).

A number of judges on the Court, including liberal Justice Stephen Breyer, suggested during the hearing, that the stance taken by the Commission could ultimately endanger the right of the Catholic Church to ordain only men as priests.

The case involves a teacher in a Lutheran parish church and school which attempted to stop her from filing a discrimination lawsuit against her employer on the basis of the church’s claim that the teacher is a religious minister.

The teacher, Ms Cheryl Perich, was an elementary teacher at a Michigan school run by the Lutheran affiliated Hosanna-Tabor Church. In 2004, she was diagnosed with the debilitating sleep disorder narcolepsy and required several months of treatment before she was able to attempt to work again.

In that time, the school filled her position with a substitute, and due to questions surrounding her ability to meet the demands of the classroom setting, strongly suggested to Perich that she not return.

Ms Perich threatened to sue the school for violating the Americans with Disabilities Act. The school responded by firing her.

The school argued that because Perich was employed by a private school affiliated with a religious organisation, her job was ministerial and religious in nature. As such, the mere suggestion that Perich violated some aspect of the Lutheran Church’s bylaws was sufficient grounds to dismiss her, and the action was not subject to the anti-discriminatory laws that govern secular employees.

They argued that her dismissal was covered by a legal doctrine known as the ‘ministerial exception’ which says religious groups don’t have to follow anti-discrimination laws in employment decisions about their leaders.

However the Obama administration, arguing on behalf of the EEOC, urged the court to embrace a line of analysis that would have virtually eliminated the ministerial exception.

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.

However, a number of justices took issue with the position, suggesting that the implications of the Administration’s stance attacked the very heart of the US Constitution’s guarantee of religious freedom,

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.”

Chief Justice John Roberts raised the issue by asking whether the administration considered anything “special about the fact that the people involved in this case are part of a religious organisation”.

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

Senior Supreme Court justice Antonin Scalia said that the Administration’s stance was “amazing”.

Justice Scalia said: “We are talking here about the free exercise clause and about the establishment clause, and you say they have no special application?”

Several justices expressed concern that the suit would involve 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 Ms 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”.

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 sceptical of the Administration’s stance.