The Harvest Family Church, the Hi-Way Tabernacle and the Rockport First Assembly of God were all damaged during Harvey, according to a lawsuit filed Monday in the U.S. District Court for Southern District of Texas. The First Assembly of God lost its steeple, roof and church van, while the other two churches were severely flooded. In addition, the Hi-Way Tabernacle serves as a FEMA staging center, sheltering up to 70 people and distributing more than 8,000 emergency meals.

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Yet the churches will not be eligible for recovery money from FEMA, which “categorically excludes houses of worship from equal access to disaster relief grants because of their religious status,” according to the lawsuit, which asks the court to declare FEMA’s church exclusion policy unconstitutional and seeks an emergency injunction preventing its enforcement.

“The churches are not seeking special treatment; they are seeking a fair shake,” the lawsuit reads. “And they need to know now whether they have any hope of counting on FEMA or whether they will continue to be excluded entirely from these FEMA programs.”

FEMA excludes buildings that provide “critical service” or “essential government services” from repair if more than half their space is used for religious programming, the suit said. Museums and zoos are eligible for relief, but churches are not.

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“If the Churches were to cease all religious activity in their houses of worship, those buildings would become assistance-eligible,” the lawsuit read.

A FEMA spokesman declined to comment on pending litigation.

This issue is not new. In 2002, President George W. Bush made news when his administration approved a $550,000 grant to a Jewish school devastated by an earthquake. After Katrina in 2005, the Bush administration said that parochial schools, nursing homes and other faith-based institutions could get federal disaster aid but that the government would not pay to rebuild houses of worship.

This week’s lawsuit comes three months after the Supreme Court decided that a church in Missouri could get government money to resurface its playground — a major religious-liberty decision that has set the stage for similar cases, some experts say.

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“The consequence is, in all likelihood, a few extra scraped knees,” Chief Justice John G. Roberts Jr. wrote in Trinity Lutheran v. Comer. “But the exclusion of Trinity Lutheran from a public benefit for which it is otherwise qualified, solely because it is a church, is odious to our Constitution all the same, and cannot stand.”

Diana Verm of Becket, a nonprofit Washington law firm that seeks to defend religious liberty, said the churches sued FEMA partly because of the Trinity case.

“This is a time of crisis in Houston,” she said. “Churches are some of the helpers, doing everything they can to get back on their feet. Yet they are denied the same relief other nonprofits are getting from FEMA.”

When FEMA provides money to communities stricken by natural disaster, not everyone can get it. For example, community centers “operated by a religious institution that provides secular activities” are eligible, according to the agency’s policy guide, but other religious institutions may not qualify.

Alex Luchenitser, the associate legal director for Americans United for Separation of Church and State, another D.C.-based nonprofit, said the Trinity decision was not applicable to the church litigation. That decision allowed a church to get funding for a nonreligious function, he said; the Texas churches are seeking money for “core facility” repair.

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“We know a lot of people in Texas are suffering, and we are sympathetic,” he said. “But the fact that something bad has happened does not justify a second wrong.” He added: “Taxpayers should not be forced to protect religious institutions that they don’t subscribe to.”

FEMA funds have been used to reimburse churches before. When money went to churches after Hurricane Katrina in 2005, officials said the decision was unprecedented, and some — including some of the faithful — wondered whether the funding was appropriate.

“The people have been so generous to give, that for us to ask for reimbursement would be like gouging for gas,” the Rev. Flip Benham, the director of the antiabortion group Operation Save America, said at the time. “That would be a crime against heaven.”

Founded more than 15 years ago, the 300-member Hi-Way Tabernacle in Cleveland worked with FEMA during Hurricanes Rita and Ike, the lawsuit said, and turned its gym into “a warehouse for the county” during Harvey. The church’s pastor said Hi-Way would do the work anyway but would like some help.

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“The Tabernacle is here to help people,” Pastor Charles Stoker said in a statement. “If our own government can help us do that, that’d be great. And if not, we’re going to keep doing it. But I think that it’s wrong that our government treats us unfairly just because we’re Christians.”