A State Department-backed conference here this week on problems of religious freedom internationally has stirred a bitter domestic religious debate and raised questions of whether the meeting amounted to improper church-state entanglement.

The religious liberty conference, which climaxed Tuesday with an address by President Reagan, was cosponsored and partially financed by the State Department, together with an interfaith coalition spear-headed by the evangelical Protestant Institute on Religion and Democracy.

It is believed to be the first time the State Department, whose role is to execute the nation's foreign policy, has teamed with domestic religious groups to cosponsor an event. Since its founding four years ago, the IRD has devoted its energies to unmasking what it perceives to be Marxist tendencies in main-line churches in this country.

Most of the 22 speakers at the conference concurred with Reagan when he said that "the most essential element of our defense of freedom is our insistence on speaking out for the cause of religious liberty."

But many of the speakers used their turn at the podium in the State Department's Loy Henderson Conference Room to attack the National Council of Churches for its efforts to develop contacts with church leaders in the Soviet Union.

Sociologist Peter Berger of Boston University charged that the stance of main-line churches toward religious liberty was "a major scandal of our time, an outrageous and disgusting phenomenon." NCC churches, he alleged, regard religious liberty "as a luxury, if not frivolous."

"Wittingly or unwittingly, the NCC is deeply involved in concealing and distorting the truth about the Soviet Union," said Peter Reddaway of the London School of Economics, in a discussion of NCC-sponsored visits of U.S. church members to Russia.

He also accused the NCC of "promoting Soviet foreign policy aims in putting the blame for the arms race on the United States."

According to the IRD's Dianne Knippers, this week's conference, attended by some 200 persons, grew out of a smaller gathering two years ago, sponsored by the IRD and the National Association of Evangelicals.

"We approached the State Department," she said, which agreed to cosponsor this gathering. The Department also arranged a $44,969 grant from the United States Information Agency to the IRD to bring religious leaders from overseas for the conference. Also enlisted as cosponsors were the American Jewish Committee, the Anti-Defamation League of B'nai B'rith and the Jacques Maritain Center, a right-wing Catholic group.

Rabbi Marc Tanenbaum of the American Jewish Committee, said his group had been assured that both the United States Catholic Conference and the National Council of Churches had also been invited to participate. "We took it as a matter of good faith that it would be a broad-based effort," he said.

In fact, neither the Catholic bishops nor the NCC was invited to join in sponsorship or planning.

Some conference speakers sought to make an issue of the fact that NCC representatives also declined the invitation to participate in the program. "Let the record show they were invited; they were begged," said the Rev. Richard J. Neuhaus.

The Rev. Arie R. Brouwer, general secretary of the NCC, said in an interview that he first learned of his "invitation" in late February when an NCC colleague showed him a conference program that listed Brouwer as a conference panelist.

Also listed were Roman Catholic Cardinals Franz Koenig of Austria, Stephan Kim of Korea and Jaime Sin of the Philippines, none of whom had agreed to participate, a Catholic spokesman said.

Brouwer declined to participate, citing reservations about church-state conflicts. "There is, I think a touch of irony in a conference on religious liberty being cosponsored by an agency of the state and selected religious groups," Brouwer wrote Elliot Abrams, who heads State's Bureau of Human Rights and Humanitarian Affairs.

"Since matters of religious liberty by definition concern themselves with points of tension between church and state, would it not be more appropriate for religious bodies to hold a conference on religious liberty completely free from any 'cosponsoring' arrangement with an agency of the state?" Brouwer proposed.

The continued criticism of the NCC during the conference itself dismayed participants, particularly those who were unfamiliar with the church politics involved. In a wrap-up open forum, University of Michigan Prof. Juan R. Cole said he was "disturbed by the frequent personal and institutional attacks . . .

"I thought the purpose of this meeting was to forge a unity and come together on the question of religious liberty," said the professor of history. "I've been really disturbed by the amount of squabbling that's gone on." He urged that "serious attention be given by the State Department to avoid this in in the future."

United Methodist Bishop Leroy Hodapp of Indiana raised similar concerns in a post-conference letter to Abrams, a copy of which was obtained by The Washington Post. Hodapp conceded the right of IRD representatives to attack the NCC.

"But when it is done in a conference cosponsored by the State Department, moral and ethical . . . questions immediately are evoked," said Hodapp, who has served on the NCC's board.

When church and state join to attack problems of religious freedom "and then use the occasion and the setting, a conference room of the State Department . . . to castigate other religious groups who are not even present, the question of religious freedom in America becomes a high agenda item," he said.