The head of a national Jewish human rights organization today said there is nothing innocent about President Reagan's involvement with right-wing Christian fundamentalists.

Rabbi Henry Siegman, executive director of the American Jewish Congress, told a national gathering of Christian and Jewish leaders that under the leadership of the Rev. Jerry Falwell and others, the Christian right has "placed themselves at the very heart of the conservative movement in America." And, he said, the Christian right has, with Reagan's blessing, "seemed to have taken control of the Republican Party" as well.

"What is particularly ominous is that all of this has happened with the support and blessing of our president," the rabbi said, adding, "There is nothing innocent about the president's involvement."

Siegman assailed as unconstitutional the contention of Falwell and other fundamentalist Protestants that this is a "Christian" nation in which non-Christians are a "deviation from established orthodoxy."

Such a view "is an arrogant and mischievous misreading of the Constitution, one that would transform America's religious minorities from a status of equality to that of tolerated guests."

Siegman's remarks, which were greeted by sustained applause, came during the second day of a four-day workshop on Christian-Jewish relations. The Protestant portion of the nearly 1,000 clergy and lay participants came overwhelmingly from mainstream churches, including the Southern Baptist Convention, rather than from New Right groups.

The conference was designed to focus on theological and philosophical understandings that could ease the way to greater interfaith amity. But in the closing days of a political campaign that has seen unprecedented involvement of religious issues, politics kept creeping into discussions here.

At Monday's opening session, heads of the nation's major Protestant, Catholic and Jewish organizations focused on the progress that has been made in interfaith relations in recent years. At the same time they acknowledged their differences on some political issues.

"It must be affirmed as we speak about our growing mutual respect that there are deep divisions," said Bishop James Malone of Youngstown, president of the National Conference of Catholic Bishops. "But we need to be in dialogue precisely because there is a polarity between us."

Speaking at an opening press conference, Malone said that on the abortion question, "the value that is attached to the unborn child is a value that is viewed differently by the participants in our dialogue. We acknowledge that, and we don't seek to make converts from Jews and Protestants."

Malone said candidates for public office "should be expected to articulate" their views on controversial issues. On abortion, he said, "we are not asking every candidate to agree [with the bishops], but we think they should say where they stand."