Outgoing Transportation Secretary Neil Goldschmidt, declaring preservation of the U.S. auto industry a national security issue, called yesterday for negotiations with the Japanese to limit sales of their cars here temporarily and for restrictions on United Auto Workers wage demands.

Announcing results of a study seven days before his term expires, Goldschmidt also said auto industry managements should make some concessions and the government should eliminate regulations burdening the auto industry. The problems of Chrysler Corp., the most financially strapped of the Big Three, don't indicate "a peculiar circumstance" but "the tip of the iceberg for this country," Goldschmidt said.

He conceded that there's nothing he can do to implement anything in the report during his remaining week as secretary, but the report could be seen as adding fuel to the industry's drive for some help from the incoming Reagan administration. Goldschmidt said he "hoped those that follow will use [the report] as best they can."

New administration officials, however, have indicated that they will oppose any aid to help a specific industry but rather will attempt to improve the economic climate for all businesses.

No other nation faced with an auto industry losing $4 billion a year "would allow that industry to be swamped . . . or bankrupted and purchased at a fire sale," Goldschmidt said.

Pumping more fuel into the heated auto issue yesterday, General Motors Corp. Chairman Roger B. Smith echoed sentiments similar to Goldschmidt's at a National Press Club luncheon. Smith said the unions must cooperate with the auto companies during their transition from large cars to small cars in an effort to compete more effectively with the Japanese.

Although General Motors has been relatively passive in the assault against Japanese imports, taking a back seat to Ford Motor Co., Smith said he would be "delighted" if the government negotiated an agreement with the Japanese to limit their imports but added that legislating quotas would be wrong.

Goldschmidt's report, which was a year in the making, said the government should negotiate an import-restraint agreement with the Japanese "which reflects the real time period it will take for U.S. automakers to accomplish the transition" from large to small cars. Goldschmidt said the length of the agreement wasn't as important as how many vehicles should be restricted, and he had no recommendations for either. He also said that no agreement should be made until the government knows what concessions labor and management will make.

Goldschmidt reportedly was one of the Carter administration officials who tried unsuccessfully to persuade the president to negotiate limits with the Japanese. However, after losing the election in November, President Carter said that he would leave the matter with President-elect Reagan.

The report also said the government should change depreciation schedules, provide refundable tax credits specifically for the auto industry or create a "reindustrialization finance corporation" to help the industry acquire capital.