President Carter's plan for peacetime draft registration was not what the Pentagon's manpower office had in mind, according to an internal Defense Department report obtained yesterday.

The report also warned that requiring the registration of men, but not women, probably would be challenged in the courts and could hinder mobilization.

The document, dated January 1980 and obtained by Rep. Patricia Schroeder (D-Colo.) under a Freedom of Information Act request, is expected to fuel the controversy over President Carter's plan to require 19- and 20-year-olds to register this year.

Since the House has refused to pass the required legislation for registration of women, Carter is now trying to persuade Congress to provide $13.3 million in fiscal 1980 supplemental funds to finance the registration of men only.

The manpower office report, written as Carter was mulling his registration decision, did not recommend peacetime registration. It noted that the Selective Service "is developing plans to conduct an emergency registration within the first 10 days after mobilization is announced."

Selective Service, in a separate report dated Jan. 16, said it would be most "cost-effective to register young people after a national emergency were declared. Carter has rejected that recommendation, partly on the ground that peacetime registration would demonstrate national resolve to the Soviet Union.

Now that Carter has settled for men-only registration, the key questions become whether Congress will provide the money and whether the courts will uphold the registration of men but not women.

The White House is pressing Congress to get around its budget ceiling for fiscal 1980 and still come up with the $13.3 million for men-only registration by transferring that amount from the Pentagon to the Selective Service. A resolution to do this is expected to be voted on next week by the House Appropriations Committee. The Senate is awaiting House action.

In discussing the risk of men-only registration being invalidated in the courts, the Pentagon report said that "an injunction arising from these suits could cause damaging delays during a period of national emergency or war."

"Extending the presidential authority to register, classify and, with congressional approval, to induct women as well as men would reduce the risk of adverse court action during a time of crisis," the report said.

"Women have proven that they can successfully serve in a large number of occupations in our peacetime military force, and also can serve successfully in large numbers in an expanded wartime force.

"Consequently, if registration or induction is reinstated and women are excluded, it is likely that sex discrimination suits would be brought against the U.S. government."

The American Civil Liberties Union has vowed to file such a suit. The Justice Department, in an opinion that differs from those of the Pentagon and the Selective Service System, has predicted that men-only registration would survive a court challenge.

At a Senate Armed Services Committee hearing yesterday, Sen. John Warner (R-Va.) said that any government plan that required the registration of women would "open the floodgate" and wash away the powers of the president and the Congress to keep women out of combat.