Secretary of State Alexander M. Haig Jr. has taken charge of the administration's sensitive talks with Japan on auto imports, planting his flag in a new policy frontier to the surprise of the Japanese and the consternation of U.S. Trade Representative Bill Brock, officials said.

Haig, who last week helped break a deadlock within President Reagan's Cabinet on the Japanese import question, presented the administration's position to Japanese Foreign Minister Masayoshi Ito in meetings Monday and yesterday, acting as the chief spokesman on the issue.

Brock -- who has expected to have the lead role in working out the auto problem -- flew back from a family vacation in Sarasota, Fla., Monday to meet with Ito, but his session lasted less than an hour and followed Ito's 3 1/2-hour meeting Monday with Haig. Ito and Haig then met before breakfast yesterday morning, and joined Treasury Secretary Donald Regan for breakfast. Brock did not attend.

Ito told reporters yesterday he hadn't realized Haig was so involved in auto policy.

Haig also talked to Ito about international energy policy this week -- an issue that was firmly lodged in the Department of Energy in the Carter administration. Haig is concerned with "pulling together" the views of other Cabinet departments on issues that involve foreign policy, a Reagan administration official said yesterday, "but that doesn't mean State is setting energy policy."

A Cabinet-level task force headed by Transportation Secretary Drew Lewis had been trying without success to find a common position on the auto import issue until last week. Then Haig, Brock and Regan joined with Lewis last Tuesday in recommending that the administration "signal" the Japanese that they should voluntarily reduce auto exports to the United States, administration sources have said.

Haig apparently moved at once to become the chief signal-caller, telephoning Mike Mansfield, the U.S. ambassador to Japan, on Friday to pass the word that he would brief the Japanese officials in Washington, sources said.

The maneuvering between the secretary of state and the trade representative may have significance beyond the internal power struggles of the Reagan administration, according to some close to the talks. Japanese trade officials were left out of Ito's Monday meeting with Haig and reportedly fear they will lose influence in the continuing U.S.-Japanese auto negotiations if Brock's role is diminished, sources said.

Japanese trade officials are reportedly concerned that Haig and the foreign ministry will push for a low limit on Japanese auto imports, perhaps below 1.5 million cars, a level that trade officials believe will be unacceptable to the Japanese auto companies, sources said.

Japanese officials have indicated that auto shipments to the United States this year are likely to total about 1.8 million cars, somewhat under last year's exports of 1.9 million cars. But the U.S. auto industry is telling Congress that tougher restrictions are essential.

President Reagan told Ito yesterday that although he is firmly committed to free trade, and opposes trade sanctions against Japan, it would be politically difficult for him to veto a congressionally enacted quota because of the rising tide of protectionism in this country, the foreign minister told reporters.

The next step is talks between the two countries, starting soon, in hopes of resolving the issue. It is not yet determined whether Haig or Brock or both will lead the U.S. side in the forthcoming discussions with the Japanese.

But Haig apparently isn't in doubt about the propriety of his involvement in trade matters. "Clearly the issue of foreign trade is a fundamental aspect of the nation's foreign policy," he told a congressional committee yesterday.

His duties and Brock's do overlap, Haig acknowledge. "As you know, the . . . trade representative himself is charged by statute . . . with the responsibility for trade policy across the board." Thus the two officials have joint responsibility, he added.

"I lean heavily on fundamental policy and the linkage and the relationships in the conduct of our affairs in a given nation, and he must, of course, pull together the central domestic concerns, the central domestic constituencies who are involved in a trade issue," Haig said.

But a spokesman for Brock said tersely: "It's our understanding that any negotiations on trade would be led by the U.S. trade representative."