Clarence Pendleton Jr., the new chairman of the U.S. Commission on Civil Rights, yesterday ushered in the new regime by releasing a report highly critical of the man who appointed him, President Reagan, and expressing his disagreement with the report's central thrust.

Noting that "only seven one-hundreths of one percent" of the president's fiscal 1983 budget is allotted to civil rights enforcement, the 68-page report criticized Reagan's proposals as "a new low point in a disturbing trend of declining support" that could make federal civil rights laws "little more than devalued pieces of paper."

Pendleton, a black Republican, noted during his first news conference that, although he signed the report, it was prepared before he joined the commission.

He called on the president to make a clarifying policy statement to end "serious perception problems" regarding the administration's position on civil rights enforcement, and to quell the competition among the "many voices" now speaking for Reagan on the issue.

Pendleton took issue with the report's contention that the budget cuts are a "tangible expression" of a diminished government commitment.

Reagan "has stated many times that he is not a racist," Pendleton said. "I believe that."

Pendleton repeatedly disagreed with positions expressed by holdover commissioner Murray Saltzman, a Democrat who is to be replaced soon, regarding the impact of the budget cuts and the drift of government policy. Saltzman said the report reflects "a fundamental shift in policy that borders on the abandonment of the 1960s' commitment to civil rights."

The report contended that total outlays for federal civil rights enforcement are about $106 million less than two years ago, when adjusted for inflation. Under the fiscal 1983 proposals, it added, the government would have nearly 25 percent less spending power for civil rights enforcement than it had in fiscal 1980.

The report goes into detail on the impact of this on key agencies. For example, the Education Department would be able to perform compliance reviews of fewer than 3 percent of the 2,500 school systems and institutions believed to be in serious violation of civil rights laws.

While the conclusions are not encouraging, Pendleton said, "The commission does not believe that civil rights enforcement problems can be corrected just by throwing money at them."

He said he will ask the commission to approve a private sector task force to study ways of improving compliance with the laws. And he indicated that government managers should find ways to use their dwindling resources more effectively.

Pendleton's was one of several controversial appointments that Reagan has made to civil rights posts. Some civil rights activists have charged that the president is trying to cripple civil rights enforcement by appointing people who oppose it or who are inept at it.

One nominee, the Rev. B. Sam Hart, a Philadelphia radio evangelist, was forced to withdraw after a storm of protest over his financial problems and his qualifications.

The White House recently announced the names of three new nominees to the commission: Robert A. Destro, general counsel to the Catholic League for Religious and Civil Rights in Milwaukee; Constantine Nicholas Dombalis, dean of the Sts. Constantine and Helen Greek Orthodox Cathedral of Virginia in Richmond, and Guadalupe Quintanilla, assistant provost at the University of Houston.

Destro has raised the hackles of pro-choice groups and civil rights activists because of his anti-abortion stance and his past criticism of the commission.

Pendleton, 51, is the first black chairman of the commission. The former head of the San Diego Urban League, he is a Washington native and a graduate of Howard University who once coached swimming there. Washington seemed "more comfortable when I was out on the streets," he said after yesterday's news conference.