The U.S. Commission on Civil Rights, half of whose members President Reagan is trying to oust, blasted the administration on the sensitive subject of education yesterday, charging that a proposed 13 percent budget cut would seriously harm programs for minority groups and the handicapped in the schools.

The report came as the Senate Judiciary Committee prepared to open confirmation hearings today on Reagan's nominees to replace three of the six commissioners. Reagan fired the three May 25 to bring the panel in line with his thinking on racial quotas and other issues.

The commission has been a constant thorn in the administration's side, and yesterday's report was another, possibly last-gasp example of this. It essentially took the anti-Reagan side in the debate over federal aid to education just as the administration has been working to improve its image on the issues of both education and civil rights.

Secretary of Education T.H. Bell said in a statement that the report "distorts and undervalues what this administration is doing for education." He also said the report was "outdated by current events before it was issued."

In a statement announcing release of the report, commission Chairman Clarence M. Pendleton said, "At a time when the nation's educational system is in jeopardy, we can ill afford to reduce the federal commitment to equal educational opportunity." In an interview later, however, Pendleton, who was appointed by Reagan, sought to put a little distance between himself and the report.

"I am not as convinced that the non-increases or budget cuts really make that much of a difference, because there will still be a gap between what local school districts have to do and what the federal government puts in," he said.

The 124-page report said the administration is seeking almost $2 billion less for education in fiscal 1984 than Congress approved for this fiscal year, and that the Reagan budget would eliminate 34 programs.

"Many of the educational programs slated for cuts are those that have met with success in improving the quality of education for the neglected and the disadvantaged," the report says. Programs slated for cuts include those that provide remedial education to children from low-income homes, Indian education, aid to minorities and women pursuing graduate study and aid to desegregating school systems.

The report calls for Congress "to examine closely the proposed cuts," but "the message of the report," Commissioner Mary Frances Berry, one of those Reagan is ousting, said at the news conference, "is that Congress needs to reject the administration's budget once again and restore these cuts, as it did last year."

Pendleton, however, did not agree. "That's an interpretation," he said. "I'm not sure that's the message of the report." Asked directly if he favors restoration of the cuts his commission's report details, Pendleton said: "I favor the wisdom of the entire budget process."

Among other things, the report noted that the administration's budget would:

* Cut $146 million from the current $3.16 billion appropriation for programs for children from low-income homes.

* Rescind $43.5 million in bilingual education funds for this fiscal year and keep funding at that reduced level next year.

* Leave aid to college students at about the current level, but tighten eligibility requirements to make students contribute 40 percent of college costs before being eligible for grants.

* Eliminate a $24 million civil rights technical assistance and training program that provides money to desegregating school systems.

In his response to the report, Bell said that most of the $2 billion in reductions "was made possible because the decline in interest rates has dramatically reduced the cost of the huge guaranteed student loan program." He said the budget proposal necessarily reflects "the national priority for economic recovery." But he said the administration "will stand by the poor, the handicapped, the minorities and the advancement of education generally."

Reagan fired the commission's previous chairman, Arthur S. Flemming, in November, 1981, and nominated Pendleton to succeed him. The new nominees are Morris Abram, 64, a New York City lawyer and ex-president of Brandeis University; John H. Bunzel, 59, a senior research fellow at Stanford University's Hoover Institution and ex-president of San Jose State University, and Robert A. Destro, 32, a Catholic University law professor.

Civil rights groups have accused Reagan of trying to stack the supposedly independent commission and stifle criticism, and the Leadership Conference on Civil Rights today is expected to urge the Senate to reject the nominations.