The U.S. Commission on Civil Rights, saying it is "distressed," has called on Labor Secretary Raymond J. Donovan to back away from plans to cancel a rule barring employers from paying membership fees in private clubs that have discriminatory policies.

The commission yesterday released a copy of an appeal sent three weeks ago to Donovan, urging that he reconsider his opposition to the regulation, which would have become final March 30.

In a letter signed by chairman Arthur S. Flemming and dated May 6, the commission said withdrawal of the regulation would be an "unwarranted" step at a time when the professional advancement of women and minorities is linked increasingly to their ability to broaden business and social ties through private clubs.

Without the rule, the commission warned, "exclusionary membership practices may be expected to become an increasingly frequent and salient barrier to equal employment opportunity. Consequently, this rule will become even more important in the future."

Three days before the rule was to have taken effect, the Labor Department announced its intention to withdraw it, contending it would cause excessive record-keeping and reporting burdens for firms that pay employes' fees in private clubs.

A commission spokesman said yesterday that Donovan had not replied to the letter. A similar appeal to J. Clay Smith Jr., acting chairman of the Equal Employment Opportunity Commission, seeking his support, also has not been answered, the spokesman said.

Officials at Labor and the EEOC had no comment yesterday on the commission's correspondence.

In announcing its eleventh-hour decision in March to withdraw the final regulation, the department contended that an executive order issued in 1965 by President Johnson was adequate to ensure against discriminatory policies by private clubs.

But the issue has continued to bubble up in civil rights circles for years. In 1975, the Treasury Department, for example, found such discrimination widespread in the banking industry and sought guidance from Labor's Office of Federal Contract Compliance Programs.

According to the commission, little guidance came from the OFCCP and, in 1979, federal financial regulatory agencies issued a policy statement encouraging financial institutions to ensure that their fee payment policies did not abet discrimination in private clubs.

At the same time, the federal financial regulators called for promulgation of a regulation by OFCCP to protect women and minorities. The rule that finally was proposed was buttressed by two supporting legal opinions from the Justice Department.

In its letter to Donovan, the commission said it does not believe the executive order adequately provides clear instructions to contractors on the question of fee payments to clubs.

"This inadequacy is compounded because OFCCP's Federal Contract Compliance Manual does not instruct its staff to review a contractor's fee payment policy to determine if it is nondiscriminatory," the letter said.

The commission also challenged Labor's position on excessive paper work requirements.

"No special documentation or filing would be required," the commission said. "The contractor would be expected to demonstrate the nondiscriminatory effect of such payments only in the course of a compliance review. This does not appear to us a major burden."