Langhorne A. Motley, assistant secretary of state for inter-American affairs, was asked recently where the Reagan administration hoped to find support for its proposed $14 million aid package for the U.S.-backed "contras" fighting to overthrow Nicaragua's Sandinista government.

"Certainly not from the churches," he replied.

Motley's biting observation reflected the fact that, to an extraordinary degree, the nation's churches and synagogues have become the focal point for opposition to President Reagan's policies on Nicaragua and El Salvador -- a grass-roots opposition with passion and political commitment not seen since the Vietnam war.

The informal coalition includes Jews and every kind of Christian -- Roman Catholic bishops and Presbyterian elders, Mennonite farmers, students and faculty members at small evangelical colleges in the South, and the more than 1,200 local churches offering sanctuary and other forms of direct and indirect aid to refugees fleeing conflict in Central America.

Since Reagan took office in 1981 declaring that the ferment in Central America was caused by a "Soviet-Cuban offensive," 17 major U.S. denominations have formally protested U.S. intervention in the region, 13 of them also condemning the U.S.-inspired and -financed military effort to destabilize the Sandinista government.

In the last year, a group backed by Sojourners magazine in Washington has collected more than 55,000 signatures on a "Pledge of Resistance" to begin nonviolent demonstrations at any sign of U.S. escalation in the campaign to destabilize Sandinista rule in Nicaragua.

Observers say the movement -- by focusing attention on moral issues and on the disparity between an impoverished nation of 2.7 million and a military and economic superpower -- also fuels growing antimilitaristic attitudes on other foreign policy and security questions, including the arms race and U.S. relations with military regimes.

The movement's political importance is acknowledged by both sides. The elected leader of the nation's Catholic bishops, Bishop James W. Malone of Youngstown, Ohio, recently remarked that he agreed with a New York Times commentator's assessment that "the difference between Vietnam and Central America is that the Catholic Church stands between us and Central America."

The State Department's Motley, commenting on Reagan's decision to compromise on contra aid rather than risk a serious defeat in Congress, said: "Taking on the churches is really tough. We don't normally think of them as political opponents, so we don't know how to handle them. It has to be a kid-glove kind of thing. They are really formidable."

The church-based network that went into action over the contra aid vote has been forming since the late 1960s, when human rights abuses in Latin America began to concern groups like the U.S. Catholic Conference, the National Council of Churches and the Anti-Defamation League of B'nai B'rith.

That concern spawned groups like the Washington Office on Latin America (WOLA), a center for information and political action that opened here in 1974, and the Council on Hemispheric Affairs.

Later, lobbying coalitions developed around broader questions of foreign, military and economic policy. One was the 120-member Washington Interreligious Staff Council. Last year one of its task forces, Interfaith Action for Economic Justice, mobilized an appeal to Congress by 49 national religious groups, urging a halt in aid to El Salvador and to the contras. Another was the Coalition for a New Foreign and Military Policy -- made up of nearly 40 church-related or secular agencies at least partly church-financed.

Until the late 1970s, South America -- Brazil, Argentina and Chile -- held the attention of these groups. What began to transform Latin American human rights lobbying in the capital into a grass-roots movement were reports of Catholic priests and nuns being attacked and killed in Central America, particularly in El Salvador. Then, in 1980, Archbishop Oscar Romero was assassinated and four female American Catholic church workers were murdered in El Salvador.

The killings not only outraged Catholics but catalyzed many Protestants. Two months after Romero's death, an Inter-Religious Task Force on El Salvador and Central America began operating in the Manhattan building that houses the National Council of Churches and the mission agencies and head offices of a number of mainline Protestant denominations.

"A lot of people in the religious community just said, 'We need to be doing something,' " said Patricia Rumer, the United Church of Christ regional Latin America secretary who has chaired the task force since last summer.

The task force lists 28 national and regional church-agency memers and says it is in touch with about 3,000 individuals and groups, including some 350 Central American task forces organized by local churches.

A coordinating group in Washington, the Religious Task Force on Central America, reaches some 2,000 people in 200 independent local churches and diocesan Roman Catholic justice and peace organizations, a task force leader, Margaret Swedish, said last summer. A separate Chicago task force coordinates the church sanctuary protest, matching refugees with churches and providing a network of contacts and escorts.

Some mainline Protestant churches also have organized Central America networks: Presbyterian Advocates, described by George Chauncey, its Washington coordinator, as a "hard core of 2,600 people who agree to get in touch with local congressmen when the Washington office signals them," was created by the 3.2 million-member Presbyterian Church U.S.A. at its 1983 general convention. A similar network run by the 1.7 million-member United Church of Christ was said by an official to be in touch with 8,000 local UCC churches.

Conservative white Christians contributed half of Reagan's second-term margin in November, but those voters remain largely silent on this issue, despite a number of appeals to get behind the president by evangelist Jerry Falwell and several others on the religious right.

Thus, when Citizens for Reagan got in touch last week with the legislative assistant for Rep. Tim Valentine (D-N.C.) -- regarded as one of 75 members of Congress who might vote either way on contra aid -- it found that the two-term congressman had been getting visits at least monthly for more than two years from church groups affiliated with the Durham-based Carolina Interfaith Task Force on Central America.

The group has spawned 14 chapters in North and South Carolina that take turns making a weekly trip to Washington to visit congressional offices. In January, a delegation that included the Presbyterian state synod executive, a Duke University religion professor and Baptist minister, and a state council of churches executive came to Valentine's House office to talk about the contra vote. Then, early in April, another group delivered a letter of concern signed by nine North Carolina United Methodist, Episcopal and Catholic bishops.

Since late 1983, Witness For Peace, also based in Durham, has taken about 1,200 clergy and lay religious leaders for two-week visits to northern Nicaraguan border areas under frequent attack by the contras.