Saying prayers during school hours is a violation of the separation of church and state. But some religious groups say a 2001 U.S. Supreme Court (search) decision clears the way for singing praises in public schools on Sunday mornings.

If the city of New York gets its way, however, such services won't continue. Next month the city will challenge the federal law, which has allowed more than two-dozen churches to obtain permits to hold their services in public-school buildings.

The churches, including Christ's Tabernacle Church (search) in Brooklyn, have been holding their Sunday morning services in schools' auditoriums and gymnasiums to accommodate their large congregations. School officials allege that the churches' services overstep the 2001 ruling.

"We are here on Sundays, there are no students in the building. This is an issue about space, purely an issue of space. Real estate in New York City is hard to come by," said Ralph Castillo of the Christ Tabernacle Church. Its building, they say, can only hold 1,000 people, which is a third of its congregation.

The city refused to comment on the case while it is pending, but New York did issue a statement saying, "Given the diverse backgrounds of all children attending public schools, the city is concerned about having any public school identified with a particular religion or congregation."

Click in the video box near the top of the story to watch a report by FOX News' Todd Conner.