Protestant and Roman Catholic church groups, facing likely defeat today in their efforts to halt new U.S. aid to the Nicaraguan rebels, have reluctantly endorsed a compromise amendment that would restrict military assistance but allow the contras to receive $25 million in nonlethal aid.

Several church-based coalitions have for two years been among the leaders in opposing aid to the rebels, known as contras, and have mobilized grass-roots lobbying campaigns against President Reagan's new $100 million aid request. Administration officials have acknowledged that the religious critics are among their toughest adversaries.

The religious groups' endorsement of the compromise offered by Rep. Dave McCurdy (D-Okla.) could be important in what is expected to be a very close vote.

The IMPACT coalition of religious activists, representing 20 national religious groups involving 71 million members, wrote to House members this week urging support for a ban on new contra funding. Rep. Lee H. Hamilton (D-Ind.) is sponsor of the ban, which is not expected to pass.

If that measure fails, the letter said, members should support the McCurdy amendment, which would delay a vote on $75 million in military aid for 90 days in an effort to start meaningful regional peace talks. The amendment would be attached to a Senate-passed measure which, if approved, would give the contras an immediate $25 million in nonmilitary aid and training.

The coalition urged members of Congress to reject the Senate-passed proposal, even if the McCurdy amendment succeeds, in a final effort to kill the aid, but Gretchen Eick, who chairs the Washington-based group, admitted the aid program will probably pass.

Eick said the church-based groups have been "working hard to get the least damaging vote," and had resisted McCurdy's amendment because it did not go far enough. "This is not the end," she said. Any aid at all "will try the patience of thousands and thousands of Americans who have dedicated themselves to saying they can make a difference."

Intense church involvement in the issue has surprised many members of Congress. "Every time we go anywhere there's some church group with a sign," complained a Republican congressional staff member. The Witness for Peace group, which has sent 2,000 Americans to visit Nicaragua, has staged "public testimony" in 100 cities centered around crosses labeled with the names of Nicaraguan civilians they say were killed by the contras.

Demonstrations sponsored by another group called Pledge of Resistance began Monday in 300 cities nationwide to oppose contra aid, drawing on a list of 40,000 people reportedly willing to engage in civil disobedience.

At the same time, an organization called Quest for Peace, led by the Roman Catholic Quixote Center of Mt. Rainier, Md., said it had raised nearly $27 million for medical and other humanitarian aid to the Nicaraguan people, matching the amount Congress provided last year for the contras.

The U.S. Catholic Conference, representing Roman Catholics, has traditionally avoided taking a stand on particular legislation, but circulated a letter last week to House members opposing any military aid in Nicaragua, either from the United States for the contras or from Cuba and the Soviet Union for the Nicaraguan government. It also protested human rights violations by all sides and urged "a much more creative and intensive effort" towards diplomatic solutions.

"Our basic line is that any aid that maintains the contras as a fighting force and thereby extends the war also serves as an impediment to the political process," said Thomas Quigley, head of the conference's Office of International Justice and Peace.

He noted that there is "still a high degree of tension" between Nicaraguan Cardinal Miguel Obando y Bravo and the Nicaraguan government, but added that the divided church there is "an entirely separate issue" from aid to the contras. The Reagan administration has cited government oppression of the church as a reason to support the contras.