The Supreme Court extended the principle of church-state separation Wednesday to shield religious schools nationwide from discrimination suits from teachers and school employees who serve as “ministers” of the faith.

In a unanimous ruling, the high court for the first time concluded the Constitution includes a “ministerial exception” that protects churches and their schools from undue interference from the government and its courts.

However, lower courts have long recognized that churches are protected from lawsuits involving their internal workings.

The 1st Amendment protects the “free exercise of religion,” and Chief Justice John G. Roberts Jr. said the state infringes on religious freedom if it forces a church or its schools to accept or retain “an unwanted minister.”

Notre Dame Law Professor Rick Garnett called the ruling "one of the court's most important church-state decisions in decades." It "protects religious liberty by forbidding governments from second-guessing religious communities' decisions about who should be their teachers, leaders and ministers," he said.

Wednesday’s ruling appears to apply to some, but certainly not all, teachers who are employed in church schools.

The justices tossed out a disability discrimination suit brought by a former Lutheran school teacher from Michigan. Cheryl Perich was a “called” teacher who taught religion as well as other classes and led her students in daily prayers. The same school had “lay” teachers who worked under contract and were not considered to be ministers of the faith.

Perich was diagnosed with narcolepsy in 2004, and after a dispute with school officials in which she threatened to sue, she was fired. She did indeed sue, alleging a violation of the Americans with Disabilities Act. The U.S. Equal Employment Opportunity Commission agreed she had a valid claim, and sued Hosanna-Tabor Evangelical Lutheran Church on her behalf.

The EEOC took the position that if there were a ministerial exception, it applies only to church school employees who “perform exclusively religious functions.” The U.S. 6th Circuit Court of Appeals agreed and ruled Perich’s suit could proceed because most of her work involved ordinary teaching of subjects such as reading and math. Only 45 minutes of her school day involved religious activities, the lower court said.

But Chief Justice Roberts disagreed and said these disputes cannot “be resolved by a stop watch.” He said Perich was “commissioned as a minister” by her church. She received a special housing allowance for those involved “in the exercise of the ministry.” And her school duties included leading chapel services.

“We conclude that Perich was a minister covered by the ministerial exception,” Roberts said, and therefore, she may not sue the church. “The 1st Amendment has struck the balance for us. The church must be free to choose those who will guide it on its way.”

A concurring opinion by Justices Samuel A. Alito Jr. and Elena Kagan said they understood the “ministerial exception” to extend equally to “Catholics, Jews, Muslims, Hindus or Buddhists” even if those religions do not use the term “minister.” The exception “should apply to any ‘employee’ who leads a religious organization, conducts worship services or important religious ceremonies or rituals, or serves as a messenger or teacher of its faith,” Alito wrote.

The 1st Amendment forbids “an establishment of religion” by the government, and it protects the “free exercise” of religion.

In the past, the court had often invoked the separation of church and state doctrine to strike down state laws that gave aid to religious schools, citing the ban on “establishment” of religion. In this case, the court ruled against government interference with religion, citing the “free exercise” clause.

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--David G. Savage in Washington

Photo: A Supreme Court ruling Wednesday shields religious schools nationwide from discrimination suits in some cases. Credit: Joshua P. Roberts / For The Times