President Reagan's remarks on religion and politics at last week's Republican National Convention have provoked strong criticism from some religious leaders.

The president's charge that those who oppose organized prayer in public schools were "intolerant of religion" was turned against Reagan by Claire Randall, general secretary of the National Council of Churches.

"To brand as intolerant of religion those with sincerely held, theologically based religious opposition to school prayer or any other matter that differs from his chosen position falls short of the standard of tolerance for the beliefs of others which must undergird religious freedom in a diverse society," Randall said.

"Does he really mean that the dozens of Baptist, Episcopalian, Jewish, Lutheran, Unitarian, Methodist and Presbyterian groups who have fought againt prayer in public schools are seeking to undermine the importance of religion in our lives?" queried Theodore Mann, president of the American Jewish Congress. He called that idea "absurd on its face."

Rabbi Alexander M. Shapiro, South Orange, N.J., president of the Rabbinical Assembly, took issue also with Reagan's assertion before a Dallas prayer breakfast that politics and religion are inseparable.

The president's views "are totally contrary to our country's tradition of separation of church and state," said Shapiro, who heads the membership organization of 1,200 Conservative rabbis. He accused the president of dividing the nation's religious groups and of "rewriting the American Constitution."

Expressing a similar view, Howard I. Friedman, president of the American Jewish Committee, noted, "It is indeed ironic that a conservative president would seek to alter constitutional principles."

He added that rigorous separation of church and state, which the First Amendment guarantees, is crucial for "a vigorous expression of religiosity" in this country.

Religious freedom and tolerance "would be severely threatened if the state became actively involved in religion in ways that Mr. Reagan and his supporters advocate," said Friedman. Prayers in public schools led "by teachers who represent authority figures to the students," as well as "publicly owned displays of religious symbols . . . produces not broad support for religion but intolerance of various beliefs."

The nation's Roman Catholic bishops have used their traditional Labor Day statement to defend their forthcoming pastoral letter on the economy, which has become controversial long before its planned release after the November election.

New York Archbishop John J. O'Connor, who heads the United States Catholic Conference committee responsible for producing the economics pastoral, denied the letter would involve a "sudden shift" in church teaching on economics.

He said the document will affirm "the great successes of the American economy" but will raise "serious and challenging" questions about economic institutions and policies.

The Women's Christian Temperance Union concluded its 110th national annual meeting in Little Rock this week by urging Congress to ban radio and television advertising of alcoholic beverages. At a minimum, the group said, the media should be required to provide equal air time to health organizations for messages on the dangers of alcoholic consumption.

People in the News: The Leadership Conference of Women Religious, the organization of executives of Roman Catholic women's religious orders, installed Sister Margaret Cafferty, a San Francisco social worker and community organizer, as president at its annual meeting in Kansas City. She succeeds Sister Catherine Pinkerton.

The parallel organization of men's religious orders, the Conference of Major Superiors of Men, chose the Rev. Stephen R. Tutas, former superior general of the Society of Mary, as president-elect.

The Rev. Paul Kittlaus, director of the Washington office of the United Church of Christ for 10 years, will become senior minister of the First Congregational United Church of Christ in Santa Barbara, Calif.

The Rev. Thomas A. Omholt, who has served churches in Brooklyn and Staten Island, is the new pastor of St. Paul's Lutheran Church, Connecticut Avenue and 36th Street NW.