By Donna Lieberman

The religious congregations at the heart of a recent controversy about the separation of church and state — nearly all of them Christian — are upset that a recent federal appeals court decision is forcing them out of the New York City public schools they have long called home.

This is an unconstitutional attack on religion, they say, claiming to have been singled out for eviction simply because their community group is religious.

As a defender of religious and civil liberties, I’m sympathetic to that argument. But it is simply wrong. In fact, allowing the churches to continue to use school facilities would actually undermine religious freedom.

The controversy began more than 16 years ago when the Bronx Household of Faith, an evangelical Christian church, challenged a city policy banning churches from using school property on weekends and after hours for worship services. In December, the U.S. Supreme Court refused to hear the congregation’s final appeal — and now about 160 religious congregations have until Feb. 12 to stop using schools as houses of worship.

This is not a total banishment of religion from public schools, mind you. Far from it. Students and the public can still use school buildings for a wide assortment of religious activities, including prayer and religious study.

Church groups can still hold religious instruction classes. This will not change.

But holding worship services Sunday after Sunday, year after year, sends the message to students and the community at large that the government favors a church. Both the church members and the community stop seeing the distinction between the church and the school. And children who are not part of the favored congregation will likely feel diminished.

As the federal appeals court that upheld the ban explained:

“When worship services are performed in a place, the nature of the site changes. The site is no longer simply a room in a school being used temporarily for some activity. The church has made the school the place where it performs its rites, and might well appear to have established itself there. The place has, at least for a time, become the church.”

The court understood that churches holding Sunday services in city schools “tend to dominate the schools on the day they use them.” They use the largest rooms or multiple rooms, often for the entire day.

Some churches use the school address on their letterhead and website, and others blanket the neighborhood with postcards listing the school as the church’s address.

For many congregations, the school is not the location of last resort — it is often a critical part of their evangelism strategy.

Indeed, an official with Bronx Household of Faith said that “church is God’s method of evangelism, and that’s why meeting in the schools is so important.”

Further, holding worship services in public schools invites discrimination. While extracurricular student clubs are open to all people and all faiths, only believers can participate in worship services. The federal appeals court found that Bronx Household of Faith “excluded people from full participation in its services if they were not baptized, were excommunicated, or if they ‘advocate the Islamic religion.’ ”

Furthermore, school buildings are not equally available to all faiths. Jews and Muslims generally cannot use school facilities during their primary days of worship because schools are largely unavailable on Fridays and Saturdays. Because Christian churches worship on Sundays, that gives them greater access to schools.

Our Constitution gives all New Yorkers the right to worship (or not) as they choose. That vital freedom depends on preserving the separation of church and state. To do so, our lawmakers must reject any legislation that lets public schools be converted into houses of worship.

Lieberman is the executive director of the New York Civil Liberties Union.