The Reagan administration yesterday pulled back from earlier criticism of Israeli Prime Minister Menachem Begin in an unusual rebuke of two high-level administration officials who are close to the president.

The rebuke was delivered by White House chief of staff James A. Baker III, who told reporters that Secretary of Defense Caspar W. Weinberger and Deputy Secretary of State William P. Clark were speaking for themselves, not the administration, when they criticized Begin in response to questions Wednesday.

"To the extent they were making value judgments with respect to Begin, Secretaries Weinberger and Clark were speaking for themselves," said Baker, who made clear that he was speaking for President Reagan. "In comments regarding restraint and moderation by all parties concerned in the Middle East, they were speaking for the administration."

Baker's statement provoked an angry call from Weinberger, who wanted to know why Baker had said what he did.

"He said he intended no repudiation or distancing," Weinberger said later. "He said he was drawing a distinction between individual actions and policy. I was talking about the policy."

Baker agreed that he was not trying to repudiate Weinberger. But when he was asked if the president thought that some of the criticisms of Begin had been too personal, he responded, "I'm confident that was the president's feeling."

Clark had described the administration attitude toward Begin as one of "disappointment." Weinberger, answering a question on a television program, said that it was "essential that there be some moderation" in the Middle East and that Begin's "course cannot really be described as moderate."

Baker did not dispute Weinberger's central point: that U.S. special envoy Philip C. Habib's efforts to achieve a Middle East cease-fire had been damaged, first by Israel's bombing of an Iraqi nuclear reactor last month and then by last Friday's bombing of Beirut, in which 300 civilians died.

The statements of Weinberger and Clark brought into the open a persistent and deepening private concern within the administration about what some see as the increasingly intransigent conduct of Begin.

But the open expression of this sentiment caused some unease at the State Department, where Secretary of State Alexander M. Haig Jr. met late Wednesday with Israeli Ambassador Ephraim Evron. A White House official said that Haig, while not disputing the difficulties caused by Begin's conduct, believed that open criticisms of the Israeli prime minister were likely to anger him and be "counterproductive to the peace process."

This view was said to be shared by Reagan. One official observed that the president had a longstanding emotional commitment to Israel and is keenly aware of Israeli suffering.

"I want an end to the whole violence," the president said in response to a question said in response to a question when he returned from riding at Quantico Wednesday. "Remember this also, that they [the Israelis] are subject to repeated rocket attacks on civilian borders themselves."

Throughout the administration yesterday, officials took their cues from Reagan and Haig, and went to unusual lengths to steer away from criticism of Begin.

State Department spokesman Dean Fischer, speaking from notes, declined to repeat or to repudiate earlier statements critical of Begin and Israel.

"At this sensitive juncture, we are not going to talk about things that are behind us," Fischer said.

Later, at the daily White House briefing, deputy press secretary Larry Speakes took a nearly identical tack. And at the Defense Department, spokesman Henry Catto insisted that "there must have been some misunderstanding" about Weinburger's target the day before.

But the criticism of Begin continued from other quarters. Senate Minority Leader Robert C. Byrd (D-W.Va.) said, "I don't think the Israeli government is pursuing a moderate course, one that is in the best interest of the United States or the best interest of Israeli itself."

And in an interview with the British Broadcasting Corp., Zbigniew Brzezinksi, national security affairs adviser in the Carter administration, said he finds it "particularly sad that the government of a democratic country would be engaging in acts which in effect are terroristic."

The bombing raid on Beirut, he said, is not appropriate for "a decent government."