When Hurricane Harvey arrived in Texas, it inflicted damage on a vast scale, upending the lives of hundreds of thousands of people. Some ended up being sheltered and fed in churches that opened their doors to the victims. But now that the federal government is stepping up to offer help, there is none for the churches that need it.

The Federal Emergency Management Agency offers grants to help victims of disasters repair and rebuild. A share of the aid is designated for government bodies and nonprofit institutions such as child care facilities, assisted living centers, homeless shelters, libraries and museums.

Under FEMA’s long-standing policy, though, this money is not available to churches and religious schools. A flooded zoo can apply for relief, but a flooded church is on its own.

That policy doesn’t look long for this world. President Trump tweeted recently, “Churches in Texas should be entitled to reimbursement from FEMA Relief Funds for helping victims of Hurricane Harvey (just like others).” He may order a change.

FEMA is also being challenged in a lawsuit by three churches contending that the agency is violating the First Amendment by penalizing nonprofit entities that have a religious mission.

The obvious defense for the FEMA policy is that while the First Amendment protects religious freedom, it also forbids governments from subsidizing churches. By this reasoning, dispensing federal disaster relief aid amounts to an establishment of religion.

But the establishment clause was not meant to deny all government help to churches. They are entitled to police and fire protection, public water and sewage access, and other general services. By the same token, they should be eligible for broad-based assistance aimed at helping communities recover from natural disasters.

Hurricanes, floods, tornadoes and the like inflict their harms on both the religious and the secular. Government rebuilding programs should be equally impartial.