The time for conservatives to direct the course of civil rights has come, says Clarence M. Pendleton Jr., chairman of the US Commission on Civil Rights. ''Reverse discrimination'' will become a reality if ''so-called liberals and pro-blacks'' continue to dominate the scene as civil rights advocates, says Mr. Pendleton, the commission's first black chairman.
Pendleton's challenge of the commission's traditional positions has caused a split within the agency.
At stake is the commission's future role in relation to its historical advocacy of court-ordered ''forced'' busing to desegregate public schools, affirmative action including ''quotas'' to bring more minorities, women, and handicapped people into the work force, and special ''set aside'' funds in the public and private sectors to contract for goods and services from minority businesses.
Openly holding out for ''staying the course'' of advocacy in preference to a turn to the right are four holdovers of the commission, led by Mary F. Berry, vice-chairman during the Carter years.
Decision time comes soon because the current five-year extension of the commission ends Sept. 30, and changes are expected in the new extension.
President Reagan backed the agency in his State of the Union address: ''In the area of fairness and equity, we will ask for the extension of the Civil Rights Commission, which is due to expire this year. The commission is an important part of the ongoing struggle for justice in America, and we strongly support its reauthorization.''
But civil rights leaders are unconvinced that Mr. Reagan's plans for the commission are compatible with their views. The Leadership Conference on Civil Rights - 157 national black, Hispanic, and Asian organizations - has denounced what it considers Reagan's attempt to purge the commission. Since he took office two years ago, he has fired the chairman, Arthur S. Flemming, replacing him with Pendleton, and commissioner Stephen Horn, replacing him with Mary Louise Smith, appointed vice-chairman. Reagan unsuccessfully attempted to dismiss the other four members during the 97th Congress. He is expected to try again during this session of Congress.
''We remaining members are under the gun,'' Dr. Berry says. ''We have the impression that we'll be fired as soon as our successors are approved by the Senate. We are in limbo until the life of the commission is extended. At that time, I feel, the President can and will replace us.''