After weeks of prodding by Republican lawmakers and the American Red Cross, the Federal Emergency Management Agency 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.

"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," said Joe Becker, senior vice president for preparedness and response with the Red Cross.

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 W. Lynn, executive director of Americans United for Separation of Church and State.

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. In those cases, "a wide range of costs would be available for reimbursement, including labor costs incurred in excess of normal operations, rent for the facility and delivery of essential needs like food and water," FEMA spokesman Eugene Kinerney said in an e-mail.

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 would dry up if the public came to believe they were receiving government handouts.

"Volunteer labor is just that: volunteer," said the Rev. Robert E. 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-Tex.) 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."

Becker said he and his staff at the Red Cross 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.

Even so, Lynn, of Americans United for Separation of Church and State, said that federal reimbursement is inappropriate.

"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.

Lynn added that he accepts the need for the government to coordinate with religious groups in a major disaster, but not to "pay for their good works."

"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 outlined the policy in a Sept. 9 internal memorandum on "Eligible Costs for Emergency Sheltering Declarations." Religious groups, like secular nonprofit groups, will have to document their costs and file for reimbursement from state and local emergency management agencies, which in turn will seek funds from FEMA.

David Fukitomi, infrastructure coordinator for FEMA in Louisiana, said that the organization has begun briefings for potential applicants in the disaster area but that it is too early to know how many will take advantage of the program.

"The need was so overwhelming that the faith-based groups stepped up, and we're trying to find a way to help them shoulder some of the burden for doing the right thing," he said, adding that "the churches are interested" but that "part of our effort is getting the local governments to be interested in being their sponsor."

A spokeswoman for the Salvation Army said it has been in talks with state and federal officials about reimbursement for the 76,000 nights of shelter it has provided to Katrina survivors so far. But it is still unclear whether the Salvation Army will qualify, she said.

The Rev. Flip Benham, director of Operation Save America, an antiabortion group formerly known as Operation Rescue, said, "Separation of church and state means nothing in a time of disaster; you see immediately what a farce it is."

Benham said that his group has been dispensing food and clothing and that "Bibles and tracts go out with everything we put out." In Mendenhall, Miss., he said, he preached to evacuees while the mayor directed traffic and the sheriff put inmates from the county jail to work handing out supplies.

Yet Benham said he would never accept a dime from the federal government. "The people have been so generous to give that for us to ask for reimbursement would be like gouging for gas," he said. "That would be a crime against heaven."

For some individual churches, however, reimbursement is very appealing. At Christus Victor Lutheran Church in Ocean Springs, Miss., as many as 200 evacuees and volunteer workers have been sleeping each night in the sanctuary and Sunday school classrooms. The church's entrance hall is a Red Cross reception area and medical clinic. As many as 400 people a day are eating in the fellowship hall.

Suzie Harvey, the parish administrator, said the church was asked by the Red Cross and local officials to serve as a shelter. The church's leadership agreed immediately, without anticipating that nearly a quarter of its 650 members would be rendered homeless and in no position to contribute funds. "This was just something we had to do," she said. "Later we realized we have no income coming in."

Harvey said the electric bill has skyrocketed, water is being used round-the-clock and there has been "20 years of wear on the carpet in one month." When FEMA makes money available, she said, the church definitely will apply.

Norma Rush, left, gets help finding clothing from Megan Dempsey, a volunteer from an Alabama church who aided victims in Mississippi.

In Ocean Springs, Miss., George Fayn carries goods at the Church of Christ, which collected clothing and supplies for victims of Hurricane Katrina.