WASHINGTON — After weeks of prodding by Republican lawmakers and the American Red Cross, the Federal Emergency Management Agency (FEMA) said yesterday that it will use taxpayer money to reimburse churches and other religious organizations that have opened their doors to provide shelter, food and supplies to survivors of hurricanes Katrina and Rita.

FEMA officials said it would mark the first time that the government has made large-scale payments to religious groups for helping to cope with a domestic natural disaster.

Civil-liberties groups called the decision a violation of the traditional boundary between church and state, accusing FEMA of trying to restore its battered reputation by playing to religious conservatives.

"What really frosts me about all this is, here is an administration that didn't do its job and now is trying to dig itself out by making right-wing groups happy," said the Rev. Barry Lynn, executive director of Americans United for Separation of Church and State.

For churches, synagogues and mosques that have taken in hurricane survivors, FEMA's decision presents a quandary. Some said they were eager to get the money and had begun tallying their costs, from electric bills to worn carpets. Others said they probably would not apply for the funds, fearing donations will dry up if the public comes to believe they were receiving government handouts.

"Volunteer labor is just that: volunteer," said the Rev. Robert Reccord, president of the Southern Baptist Convention's North American Mission Board. "We would never ask the government to pay for it."

When Hurricane Katrina devastated New Orleans and the Gulf Coast, religious charities rushed in to provide emergency services, often acting more quickly and efficiently than the government. Relief workers in the stricken states estimate that 500,000 people have taken refuge in facilities run by religious groups.

In the days after the disaster, House Majority Leader Tom DeLay, R-Texas, and other Republicans complained that FEMA seemed reluctant to pay church groups. "There are tons of questions about what is reimbursable, what is not reimbursable," DeLay said Sept. 13, noting that Houston alone had "500 or 600 churches that took in evacuees, and they would get no reimbursement."

Joe Becker, senior vice president for preparedness and response with the Red Cross, said he and his staff also urged FEMA to allow reimbursement of religious groups. Ordinarily, Becker said, churches provide shelter for the first days after a disaster, then the Red Cross takes over. But in a storm season that has stretched every Red Cross shelter to the breaking point, church buildings must for the first time house evacuees indefinitely.

"I believe it's appropriate for the federal government to assist the faith community because of the scale and scope of the effort and how long it's lasting," he said.

Lynn disagreed. "The good news is that this work is being done now, but I don't think a lot of people realize that a lot of these organizations are actively working to obtain federal funds. That's a strange definition of charity," he said.

"We've never complained about using a religious organization as a distribution point for food or clothing or anything else," Lynn said. But "direct cash reimbursements would be unprecedented."

FEMA officials said religious organizations would be eligible for payments only if they operated emergency shelters, food-distribution centers or medical facilities at the request of state or local governments in the three states that have declared emergencies: Louisiana, Mississippi and Alabama.