The Reagan administration's top antitrust official suggested yesterday that he would not oppose most joint ventures between this country's troubled automobile manufacturers.

Although William Baxter, the assistant attorney general for antitrust, said that joint ventures involving General Motors Corp. might violate antitrust laws, other joint projects involving the other three major U.S. auto manufacturers would be likely to win Justice Department approval. GM has more than 40 percent of the domestic auto market.

The question was raised during a press conference in light of the revelation this week that the Justice Department permitted the expiration of key provisions of a 1969 Justice Department consent decree with the auto companies and their trade association.

Those provisions barred the companies from sharing technological information on emission controls and from filing joint statements before regulatory agencies.

Baxter also said he is considering dropping other parts of the 1969 consent decree dealing with competition in the auto business because of "the condition of the industry and because the number of approaches now being taken toward attaining tolerable levels of discharge of the various components of automotive pollution has increased."

Pressed about the policy implications of the consent decree decision, Baxter emphasized the changed state of the industry since the decree was signed 12 years ago. "A joint venture by a group of automobile companies that have something over 90 percent of the market is a rather different thing than a joint venture today, by two automobile companies not including General Motors, for example," he said.

"In the light of 1981 circumstances of the automobile industry, it seems to me predictably difficult to convince anyone" that any cooperation between any two automobile companies is necessarily harmful, he said.

Therefore, Baxter was suggesting, as he did while leaving the press conference that a Ford Motor Co. and American Motors Corp. venture, for example, would not alarm the Antitrust Division. Those two companies control less than one-fifth of the domestic market.

On other matters, Baxter said he has not finished preparing a second amendment to the Senate telecommunications bill. That amendment, which he said will assure long-distance competitors of American Telephone & Telegraph Co. access to the phone company's local network, will be presented soon to Congress, he said.