The Reagan administration is once again debating what position to take on a controversial civil rights case, but this time there is a new voice arguing for tough federal enforcement.

Clarence M. Pendleton Jr., President Reagan's new Civil Rights Commission chairman, has launched a strong attack on the ruling by a federal appeals court because he says it would limit the reach of civil rights laws protecting women if it is allowed to stand.

His efforts have delighted women's and civil rights groups, who earlier expressed fears that the black Republican would be relatively passive about enforcing laws against sex discrimination.

The decision that troubles Pendleton was handed down July 7 by the 4th U.S. Circuit Court of Appeals in Richmond. It held that the University of Richmond's intercollegiate athletics program was exempt from federal civil rights law because it receives no direct federal aid. Only programs receiving federal funds "specifically earmarked" for them are covered, the ruling said, adding that the Education Department cannot even investigate possible violations until it has shown that a program gets direct federal money.

Pendleton wrote a strongly worded letter dated Aug. 10 to Attorney General William French Smith and Education Secretary Terrel H. Bell, warning them that the decision "would decimate civil rights protection in education" under Title IX of the Education Amendments of 1972. Title IX guarantees women equal access to educational resources, including athletic programs.

The Education and Justice departments are now studying whether to appeal the decision to the Supreme Court. Justice Department officials would not comment on the case, but sources at the Education Department say the general counsel's office would like to let the ruling stand. The two agencies have sparred previously over the administration's position in the application of civil rights laws to educational institutions.

The issue will undoubtedly end up in the Supreme Court, since two federal appeals courts have reached opposite conclusions in separate cases in the area.

In his letter, Pendleton said the Richmond court's ruling would "jeopardize protections" for women under the 1964 Civil Rights Act and the Rehabilitation Act of 1973, and could even "undermine the department's authority" in racial discrimination cases.

This decision, Pendleton wrote, would have several consequences if upheld:

* It would permit sex discrimination in athletic programs that get indirect federal money, such as funds to build gymnasiums.

* It would eliminate civil rights protection where federal money is allocated by state governments, such as the new educational block grants.

* It would narrow the definition of federal aid to exclude student grants and loans, a position advocated by the Reagan Education Department.

Ignoring the last issue, Pendleton said that the court's approach "could involve substantial federal support for sex discriminatory activities, implicate federal agencies in constitutional violations and make residual Title IX protections very difficult to enforce." The ruling's "illogical restrictions on investigations could undermine the department's authority to combat race, as well as sex, discrimination," he added.

Barbara Stein, who chairs the nonprofit National Coalition for Women and Girls in Education, said of Pendleton's arguments: "We're extremely pleased; he picked the right side."

Pendleton asked Bell and Smith to let him know whether the case will be appealed to the Supreme Court. An Education Department spokesman said a decision is not expected much before the court's Sept. 7 deadline.

The Richmond court's verdict has been directly contradicted, and Pendleton's view upheld, by another important federal appeals court ruling, this one in the 3rd Circuit. On Aug. 12, that court held that Title IX applies to just about every program at a Pennsylvania college.

The decision in the case, Grove City College v. Bell, said the private Christian school comes under the law because most of its students pay their tuition from federal grants or loans.

Even though the college gets no other direct or indirect federal aid and has never been accused of a civil rights violation, the court said all student aid could be cut off if the college refuses to pledge compliance.

Since 1977, the college has refused, as a matter of principle, to sign such pledges. Its case has become something of a cause celebre among conservatives as an example of federal intrusion. School officials called the court's ruling "frightening" and are expected to appeal.

The administration took more than a year to formulate its position in that case, with the Education Department supporting the college on "political" grounds and the Justice Department supporting the traditional definition. In the end, the administration said colleges whose only federal aid is guaranteed student loans should be exempted from the laws prohibiting discrimination in federally supported programs.

Pendleton, the commission's first black chairman, is a Washington native but continues to live in San Diego, coming here for meetings. He was head of the San Diego Urban League when he was named to succeed Arthur S. Flemming, whom Reagan fired in November, 1981. Flemming, a Republican, had criticized Reagan's budget cuts, school desegregation policies and what he said was a reluctance to enforce affirmative action programs.