The U.S. Civil Rights Commission voted 5 to 2 yesterday to reject the idea of comparable worth -- requiring women to be paid the same as men who perform jobs with similar effort, skills and responsibilities -- and to urge Congress and federal agencies also to reject it.

While acknowledging that women still earn about 40 percent less than men, the commission's Reagan-appointed majority adopted a draft report concluding that sex discrimination can best be remedied through the Equal Pay Act and Title VII of the Civil Rights Act of 1964, which prohibits job discrimination based on sex or race.

The panel's majority also rejected suggestions that objective comparisons can be made between similar jobs performed primarily by men or by women to determine their proper wage rates. The report said, "Merit, seniority, quality of production and collective bargaining also affect wages," in addition to possible lingering discrimination against people in jobs, such as nursing and clerical work, traditionally performed by women.

The anticipated vote prompted an immediate angry reaction from labor and women's groups. "The Civil Rights Commission is attempting to rewrite history and to ignore the fact of overwhelming evidence of pay discrimination against working women in traditional jobs like secretary, librarian and nurse," said Gerald W. McEntee of the American Federation of State, County and Municipal Employes.

Ellen Stein, chairman of the National Committee on Pay Equity, said the commission was urging women to enter "traditionally male jobs and educational programs if they want higher pay" while the Reagan administration is "fighting affirmative action which would make previously inaccessible jobs available for women . . . . "

The report says that statistics showing that women earned only 64.5 percent of what men earned in 1983 cannot be explained solely by discrimination against women. It said the gap could be attributed to "the effects on women of socialization in the home, and the role women play in the family generally, which affect their choices of jobs, career expectations and participation in the labor force . . . . "

"There is sex-based discrimination in America, but it is declining," Vice Chairman Morris B. Abram said in a statement explaining his vote to reject the concept. "The repetitious charge that women earn only 60 percent of what men earn in this country obscures the significant fact that women work less hours, have less seniority and work more intermittently."

"Employers should be held accountable for their individual discriminatory acts or policies," said commission Chairman Clarence M. Pendleton Jr., "but not, as comparable-worth advocates would have it, for 'societal discrimination,' or simply the choice of lower-paying jobs by certain women based on anticipated child-rearing responsibilities that they choose when married."

Last year Pendleton said he considered comparable worth to be the "looniest idea since 'Looney Tunes' came on the screen" because it would "restructure our free-enterprise system into a state-controlled economy under the guise of 'fairness.' "

The commission's two Carter administration holdovers, Mary Frances Berry and Blandina Cardenas Ramirez, voted against the report, and Commissioner Francis S. Guess abstained. Guess later explained that he felt he had a conflict of interest because he serves as Tennessee's commissioner of labor.

Berry and Ramirez acknowledged that the experts whom the commission consulted could not determine if any part of the difference between the earnings of men and women is attributable to discrimination. But they concluded that while comparable worth should be used carefully, it is "an important tool in the arsenal for attacking employment discrimination."