As President Reagan struggles to gain acceptance of his El Salvador policy, he finds a major part of his opposition coming from religious leaders. ''Most mainline Protestant denominations are on record with policy statements , and almost without exception they specifically call for an end to military aid ,'' says Beverly Keene, coordinator of the Inter-Religious Task Force on El Salvador and Central America based in New York.
Churches also are vocalizing their opposition in congressional testimony, lobbying, local campaigns to build public awareness, and even court action. A suit (Crockett v. Reagan) brought by some members of Congress charges the administration with violating the 1973 War Powers Act. The plaintiffs are supported by the National Council of Churches (NCC), United Presbyterian Church, Church of the Brethren, Unitarian Universalist Association, and other denominational agencies as well as Roman Catholic religious orders.
Already disturbed by the social injustice they see in El Salvador, the churches were shocked into action by the assassination of Archbishop Oscar Romero on March 24, 1980. The killing on Dec. 2, 1980, of four missionaries - laywoman Jean Donovan and Sisters Ita Ford, Maura Clarke, and Dorothy Kazel - further angered them.
The anniversaries of the slayings are becoming occasions to spotlight Central American issues. This past March 18-27, the Inter-Religious Task Force and other groups sponsored an observance of Central America week.
Miss Keene also reports that some churches are offering sanctuary to Salvadorean civilians who are denied refugee status in the US and are threatened with deportation - another point of tension with the administration.
On many issues, church lobbying goes unheeded, but it is having an impact regarding El Salvador, observers say. ''The churches are an influential and powerful voice,'' says Robert Dockery, foreign affairs aide to Sen. Christoper Dodd (D) of Connecticut, an administration critic. He says the senator's mail runs ''4 or 5 to 1'' against the administration, an indication of local support for national church leaders.
Though some individuals in the religious community support the Reagan policy in El Salvador, apparently few if any groups give public, organized backing.
Penn Kemble, a leader of the Institute on Religion and Democracy, says his group opposes the Inter-Religious Task Force for being too sympathetic to the El Salvador guerrillas. But he says his group has not taken a stand explicitly supporting the administration's policy, and he does not know of any religious group that has.
The churches' call for negotiation and reform, rather than use of arms, has drawn a reaction from the administration. Secretary of State George P. Shultz has charged that some church leaders seem to favor Marxists, and Vice-President George Bush has raised a similar complaint.
In congressional testimony, Catholic Archbishop James Hickey of Washington, D.C., responded: ''We reject the innuendo suggesting that church policy in Central America serves Marxist interests. . . . We do not deny the existence of an international dimension to the conflict, but we do reject the idea that it is the fundamental issue at stake.''
President Reagan, defending his policy in a radio interview May 5, said many Americans ''just do not have the information,'' and some do not even know where El Salvador and Nicaragua are. But church critics escape that charge.
Churches also give weight to messages such as one in April from the Latin American Council of Churches to the NCC, which accused the Reagan administration of ''backing up a corrupt and inhuman regime'' in El Salvador.