A federal appeals court has ruled that New York City can ban churches from using public school facilities for Sunday worship services and does not violate free speech.

The 2-1 decision by the 2nd U.S. Circuit Court of Appeals overturned a lower court ruling that allowed the Bronx Household of Faith to hold services in a public school. The justices said that could unconstitutionally convert schools into state-sponsored Christian churches on weekends. An attorney representing the church said they would appeal the ruling.

It means that dozens of churches that rent public school buildings in New York City could face eviction by the end of June. The Department of Education said it's reviewing how to implement the decision. The city said it has no intention of immediately evicting the groups. However, they may be asked to cease using school buildings by the end of June.

"We are very pleased with the Court's decision today in this longstanding case, which, reversing the lower court, upholds the Department of Education's policy not to allow public schools to be used for congregational worship services," said city attorney Jane Gordon in a written statement. "The Department is quite properly concerned about having any school in this diverse city identified with one particular religious belief or practice."

Jordan Lorence, senior counsel for the Alliance Defense Fund, blasted the ruling and called it "very, very disappointing."

"If we do not get an emergency stay, the churches could be thrown out by the school district," Lorence told Fox News Radio. "They might be meeting on the street."

Lorence said they hope the court will grant a longer stay so that churches can continue to rent public buildings.

"The religious groups are not seeking special treatment, but equal treatment," Lorence told Fox News Radio. "It would be a tragedy if these churches that serve the communities would be tossed out and be made homeless by this anti-religious policy."

But the Court determined that allowing churches to use schools resulted in an "unintended bias in favor of Christian religions" - since most Christian churches worship on Sunday.

"Jews and Muslims generally cannot use school facilities for their services because the facilities are often unavailable on the days that their religions principally prescribe for services," Judge Pierre Leval declared. "At least one request to hold Jewish services (in a school building used for Christian services on Sundays) was denied because the building was unavailable on Saturdays. This contributes to a perception of public schools as Christian churches, but not synagogues or mosques."

Judge Leval also took issue with the evangelical church's membership.

"Bronx Household acknowledges that it excludes persons not baptized, as well as persons who have been excommunicated or who advocate the Islamic religion, from full participation in its services." Leval wrote.

But it all boiled down to a key point, the judges decided.

"In the end, we think the board could have reasonably concluded that what the public would see, were the Board not to exclude religious worship services, is public schools, which serve on Sundays as state-sponsored Christian churches," Leval wrote.

One of those churches that could be homeless is The Journey Church, an evangelical congregation of about 1,000 people that meets in four different public school buildings.

"For us, it's always been about having equal access that any other secular organization might have," said Kerrick Thomas, one of the church's pastors. "I think the fear a lot of people have is that a church meets in the school and they'll be proselytizing - and it'll appear that the school is promoting the church. But that's not the case."

The Journey Church was founded nine years ago and for many of those years, the congregation has worshipped in public school buildings. Thomas said churches are not given any favors. They pay thousands of dollars in rent - and must abide by the same rules as any other organization.

"There are no special benefits given to churches," he told Fox News Radio.

Nevertheless, Thomas said they've developed positive relationships with every school they've rented - and they've gone above and beyond to help students.

"Our commitment has always been to leave the schools in better shape than when we got there through any way we could help and support," Thomas said, adding that in many instances they've assisted schools anonymously.

In one case, the church provided school supplies and computers for under-privileged children. Another wanted to perform a play but the school lacked theatrical equipment. So the church provided a sound and lighting system.

"We just did that because we wanted to help out," Kerrick said. "We believe in what the schools are doing."

But the Court determined that allowing churches to use public schools would send the wrong signal to the public.

"When worship services are performed in a place, the nature of the site changes," Judge Leval wrote. "The place has, at least for a time, become the church."

Whatever happens, Pastor Thomas said they will continue to minister to the city.

"We'll find a place and we'll work hard," he said. "I'm confident we'll find a home - but it's going to be difficult."