President Reagan's three nominees to the U.S. Commission on Civil Rights encountered strong opposition on the Senate Judiciary Committee yesterday in contrast to the support they enjoyed at hearings two weeks ago.

Three Democratic committee members and one Republican, Sen. Charles McC. Mathias Jr. of Maryland, led the counterattack. They were joined by sharp condemnations of the president and his civil rights record from such witnesses as Dr. Arthur S. Flemming, a former chairman of the commission, Julian Bond, a Georgia state senator and civil rights activist, and Kathy Wilson, president of the National Women's Political Caucus.

Albert Shanker, president of the American Federation of Teachers and the lead witness in support of the president's nominees, said that he objects to most of the administration's civil rights policies and would "like to see this administration replaced in 18 months."

At the previous committee confirmation hearing on the nominations two weeks ago, Republican committee members, led by Chairman Strom Thurmond (R-S.C.) and Orrin G. Hatch (R-Utah), controlled the session by emphasizing the credentials of the nominees.

The nominees are Morris Abram, a long-time civil rights lawyer, John H. Bunzel, a senior fellow at the Hoover Institution at Stanford University, and Robert A. Destrow, a law professor at Catholic University, and were named by Reagan to replace three commissioners he fired.

The Republicans argued that civil rights groups were opposing the three only because, like Reagan, they oppose quotas and busing.

Yesterday, however, committee Democrats, led by Sens. Edward M. Kennedy (D-Mass.), Joseph R. Biden Jr. (D-Del.) and Howard M. Metzenbaum (D-Ohio), took charge of the hearing and changed the topic of debate from the nominees' qualifications to whether Reagan is trying to "stack the commission" and compromise its independence.

"With all due respect to my friend from Utah, I really am unwilling to allow the center-right to set the parameters of this debate," said Biden, a long-time opponent of busing and quotas who also opposes the nominees.

"This debate is not about busing, not about quotas," he said. "That is a smokescreen . . . . The administration knows if we ever focus on its civil rights policy, then white America will find its activities abysmal.

"So what it does is it goes out and it picks the two things that whites and many in black America disagree with , busing and quotas, and says the only reason why there's any opposition to these people is busing and quotas. That is unadulterated malarkey."

Mathias echoed Biden's sentiments, saying that the president has the power to make the changes in the commission but has exhausted his "lubricant of good will" on civil rights.

Metzenbaum said the credentials of the nominees did not matter because the three are "tainted by the firing of the three current commissioners . . . . The issue is the independence of the commission."

Witness testimony also centered on the commission's independence.

"The Commission on Civil Rights should not be converted into a staff agency in the executive branch with its members appointed by whatever administration may be in power and subject to the administrative direction of that administration . . . ," said Flemming, the immediate past chairman, who submitted for the record a statement opposing the nominations from nine former commission members, including six Republicans and all the former chairmen.

At the July 13 hearings at which the three nominees testified, Thurmond and Hatch made long statements in support of them.

But yesterday the opposition carried the day, with Thurmond absent for most of the hearing and Hatch unable to get witnesses to shift from the issue of the commission's independence to the nominees' credentials.