Boston — 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.''
Dr. Berry says her group recommends steps to prevent any future sudden purge of the commission:
* Extend its term from five to 15 years.
* Appoint commissioners for six-year terms, with two members appointed every two years.
* Give it power to subpoena documents beyond its present ''limited'' authorization.
* Provide more money to meet the demands of increased duties. The commission originally was set up to protect black rights. But it now is also responsible for women, other minorities, the aged, and the handicapped.
Trapped between the warring factions are staff members, basically steeped in the liberal tradition. They are headed by John Hope III, acting director. ''We stay out of the politics of the situation,'' says Mr. Hope, who is temporary until the commission selects a permanent director, subject to approval by the Senate. ''So far no significant problems have arisen for us, and no projects have been jettisoned. Mr. Pendleton has only one vote and no executive authority. The chairman is the official spokesman for the commission, however, and his word is quite influential.''
Pendleton has been the lone member to publicly oppose recent commission positions - his vice-chairman has voted with the holdovers. The issues he has protested include:
* A commission vote Oct. 12 to continue its support of court-ordered busing to achieve school desegregation.
* A 104-page report Nov. 23 that endorsed affirmative action to correct the ''alarming'' racial, sexual, and ethnic bias that exists throughout the nation ''at every age level, at every educational level, at every skill level,'' and is causing an increasingly high level of unemployment among minorities.
* A Dec. 7 statement that criticized Reagan's attempts to cut aid to schools and colleges, and called the US Department of Justice support of ''voluntary desegregation'' a step backward ''to pre-1954 standards.''
* A report announced Jan. 11 criticizing Reagan's opposition to affirmative action in two civil rights cases - New Orleans police and Boston police and firefighters.
Pendleton says he agrees with the holdovers and staff on one point: Reagan ''has to develop a clear and specific civil rights policy'' in order provide direction to the commission. And he insists, ''I believe that conservatives have to lead the way of assuring equal access to every American, to ensure that there are no protected classes.''