Civil rights lawyers asked a federal judge yesterday to hold President Reagan's choice to head the Equal Employment Opportunity Commission in contempt of court because he has violated timetables for enforcing civil rights laws in his current job.

Clarence Thomas, now head of the office for civil rights at the Department of Education, acknowledged that he ignored the court-ordered time limits in some cases but said he did so in hopes of negotiating settlements.

Thomas' Justice Department attorney, Richard A. Levie, and two of Thomas' regional office heads argued that the timetables were unrealistically strict and impossible to meet.

In 1975, U.S. District Court Judge John H. Pratt ordered the government to comply with specific timetables for processing complaints after attorneys for black parents complained that the then-Department of Health, Education and Welfare was slow in enforcing racial discrimination laws in southern schools and colleges. The case was filed in 1970, and groups representing women and the handicapped later joined it.

Pratt's order gave the government 90 days to investigate a complaint, 90 days to negotiate a settlement and 30 days to commence an enforcement action. It was extended in 1977, with the government's consent.

Enforcement action could be a cut-off in U.S. funds or referral to the Justice Department for a possible suit. Thomas said yesterday that he has not been sending schools letters of complaint recently within the timetable requirements. He said he prefers to continue negotiating.

Elliott Lichtman, attorney for the black parents, filed the contempt motion last spring against Terrel H. Bell, the new secretary of education, and his civil rights chief. Thomas, 33, got the education job a short time later, and President Reagan announced last month that he would be nominated for the EEOC post.

The hearing offered a glimpse of Thomas's 1,000-member bureaucracy and its evolving workload. A recent Department of Education study showed, for instance, that complaints about discrimination against the handicapped have climbed sharply in recent years and total 51 percent of those filed.

The study also showed vast differences in the time various regional offices took to process different stages of discrimination complaints and that the productivity of civil rights investigators has fallen dramatically.

At one point, Kenneth A. Mines, the Chicago regional office director, acknowledged that investigation of a 1976 complaint about sex discrimination in the University of Michigan's athletic program has not been completed.

Thomas said under cross-examination by Lichtman that he had not accepted the study's many recommendations to improve compliance because the report is not final.

In his prehearing motion, Lichtman said David Tatel, who held Thomas' job during the Carter administration, would testify that the timetables are workable. He is scheduled to appear when the hearing continues today.

Lichtman argued that since the government agreed to the 1977 consent decree, it is too late for government lawyers to say the timetables are unworkable. But Pratt agreed to allow lengthy questioning of Thomas and the other witnesses.