For perhaps the first time since President Reagan took office, the civil rights movement has split over one of his actions, with three major Jewish organizations and the American Federation of Teachers refusing to join blacks and other groups in opposition.

The immediate issue is Senate confirmation of Reagan's three new nominees to the U.S. Commission on Civil Rights. The broader issue, as often in the past when these groups have disagreed, is quotas.

When the Leadership Conference on Civil Rights met on the nominations earlier this week, the Anti-Defamation League of B'nai B'rith, the American Jewish Committee and the American Jewish Congress, together with the AFT, refused to agree to a statement in opposition to Reagan's three choices, one of whom, Morris Abram, formerly headed the Jewish Congress.

The statement was finally issued, not in the name of the conference, but on behalf of 14 signing organizations. Conference officials later estimated that about 30 of the 160 member groups will not agree to the statement.

Conference chairman Benjamin L. Hooks, executive director of the NAACP, urged issuance of a statement at an executive committee meeting Wednesday. The lone Jewish group on the executive committee, the Anti-Defamation League, resisted but was outvoted, 14 to 1.

In the past, the conference has rarely issued statements from which member groups dissented.

The statement, under the conference's letterhead, said only that the "undersigned organizations" subscribed to the statement because of "unanimity not having been reached by all constituent groups." It did not mention quotas, saying instead that "our deep concern is to prevent the president from subverting the civil rights commission's historic independence and integrity."

Many Jewish groups have traditionally opposed quotas because quotas have historically been used to restrict Jews. Labor unions, the targets of quotas in some affirmative action cases, have also resisted them. The one major Jewish group supporting the statement is the Union of American Hebrew Congregations, a group of reformed Jews, which supports quotas. The group includes Rabbi Murray Saltzman of Baltimore, one of the Civil Rights Commission members that Reagan is seeking to replace.

Reagan fired three commission members May 25 and nominated successors who share his opposition to racial quotas: Abram, a former president of Brandeis University; John Bunzel, a senior research fellow at Stanford University's Hoover Institution, and Robert A. Destrow, a Catholic University law professor.

"The American Jewish community is a very pluralistic community," said Nathan Perlmutter, who heads the Anti-Defamation League. "Our view is the basic issue here really is that the president's nominees are known to be against racial quota systems and are presumed to question whether racial busing is an effective tool toward ending racial segregation. We believe one's opposition to racial quotas should not disqualify them from being members of the U.S. Civil Rights Commission. We feel questions being raised about procedures are smoke screens.

"If these people were carbon copies of the people now on the commission there would be no question about their serving from civil rights groups," Perlmutter said. "The core of civil rights is that one not be discriminated against on the grounds of race, sex, religion. That these nominees oppose quotas is convincing evidence that they are advocates of civil rights. Those who would deprive them of the opportunities to serve are sponsoring civil wrongs."

"It is unfortunate that the Jewish community has decided not to support the statement," said Maudine Cooper, vice-chairman of the Urban League. "We are not addressing the qualifications of the nominees but the independence and integrity of the Civil Rights Commission. I hope those groups are not reflective of the Jewish population at large."

"Nathan Perlmutter is a fanatic on this subject," said Joseph L. Rauh Jr., counsel to the Leadership Conference, who took part in the Wednesday meeting. "We can't call it a Leadership Conference statement because the majority of Jewish groups are following his lead and we don't have unanimity. Nevertheless, the other groups have the right to get together."

"What is at risk here is whether the conference continues to be a strong functioning voice of civil rights," said Elaine R. Jones, Washington counsel to the Legal Defense Fund, formerly the NAACP Legal Defense Fund. "But there is still a strong commitment to keep the conference functioning as a strong voice of civil rights."

"We have an honest difference of opinion as to propriety of the president taking action that he did," said Hyman Bookbinder of the American Jewish Congress. " . . . . But there does come a point where Jewish and some labor groups say the president is using the power that is legitimately his and he has decided to replace them. The next issue is to decide whether they are qualified to serve, and that should not be decided because of opposition to quotas."