The Reagan administration opposes a House bill that would require federal agencies to document their efforts to comply with equal-employment laws, Equal Employment Opportunity Commission Chairman Clarence Thomas testified yesterday.

Thomas said the proposed Federal Equal Employment Opportunity Reporting Act would deprive the EEOC of the flexibility it needs to help different departments eliminate barriers to the hiring and promotion of minorities and women.

"You can't have the same set of rules for the Defense Department as for the EEOC," Thomas told the House Education and Labor subcommittee on employment opportunities.

Thomas also said any legislation regulating affirmative action in government should apply to the 38,000 people employed by Congress.

The legislation sponsored by Rep. Matthew G. Martinez (D-Calif.), the subcommittee chairman, says affirmative action has not been given a high enough priority to eliminate effects of past and present discrimination in federal jobs.

It would require federal agencies to file reports with the EEOC on their compliance with the equal-employment act, including analyses of applications, hiring, training and promotions as well as goals and timetables to correct any problems that are revealed.

Martinez accused the EEOC of undermining civil rights laws and gutting its own regulations. He said the administration has rejected goals and timetables even though the Supreme Court has upheld such means of achieving a balanced work force.

Thomas acknowledged that discrimination exists in the federal work force and said goals or timetables may be appropriate in some cases. But he said the Martinez bill is not needed because the EEOC is working with department heads to identify problem areas and eliminate inequities.