President Reagan yesterday expressed sympathy for Israel's motivations in its June 7 raid on an Iraqi nuclear reactor and said he understood why Israeli leaders "might have sincerely believed it was a defensive move."

At his first news conference since March 6, the president said that Israel "had reason for concern in view of the past history of Iraq, which has never signed a cease-fire or recognized Israel as a nation."

Reagan's words were similar to those used by Israeli diplomats in defending the raid, which severely damaged a uranium-based reactor near Baghdad.

The president said he had not reached a conclusion on whether Israel's use of U.S. airplanes in that raid violated an agreement with the United States to use U.S. arms solely for defensive purposes. He suspended the sale of four F16 fighter-bombers to Israel after the raid, pending a review, but the action is not expected to be permanent.

Yesterday, the president muffled his earlier criticism of Israel and took advantage of three separate opportunities to display sympathy for the Israeli position.

"It is difficult for me to envision Israel as being a threat to its neighbors," Reagan said. "It is a nation that from the very beginning has lived under the threat from neighbors that did not recognize its right to exist as a nation."

Though the president began his session with reporters by reading a statement on his economic program, foreign policy dominated much of the news conference. In response to questions, Reagan contended:

The situation in Poland "is to be quite tense for some time now," because "the Soviet Union is faced with a problem of this crack in their once Iron Curtain and what happens if they let it go."

It is in the best interests of the United States to aid Pakistan, because that nation is "in a very strategic position now in view of what has happened to Afghanistan." But he refused to say whether Pakistan had given the United States any assurances that it will not build an atomic bomb.

Nuclear war is "a frightening posibility," and it is not possible to say whether a tactical nuclear war in Europe could be kept from spreading into a global thermonuclear war.

"I try to be optimistic and think that the threat of both sides would keep it from happening, and yet, at the same time . . . history seems to be against that," he said.

The president made at least one major factual error in his discussion of foreign policy issues, and one statement that was puzzling. The latter was a statement that a nuclear nonproliferation treaty is basically unenforceable because "it doesn't lend itself to verification." Most nuclear plants are above ground and are considered easily verifiable.

The error came when, in still another favorable reference to Israel, Reagan described as "offensive weapons" the Syrian missiles in Lebanon that Israel wants removed.

"There's no question about the direction in which they are aimed," Reagan said.

The weapons are surface-to-air (SAM) missiles used for anti-aircraft purposes.

Reagan refused to give up on the difficult mission of U.S. envoy Philip C. Habib, who has made four trips to Syria in what until now has been an unsuccessful attempt to convince Syria to remove the missiles. Saudi Arabian Foreign Minister Prince Saud Faisal said earlier this week that the June 7 raid could have a negative effect on Habib's efforts.

Asked whether the Habib mission had been permanently damaged, Reagan replied, "I hope it isn't." He said Habib had done "a miraculous job" in preventing war between Syria and Israel in Lebanon. Unless Habib returns home and says "I give up," Reagan added, he would continue to believe that the envoy's mission would succeed.

Reagan said that all of the recent events in the Middle East, taken together, "demonstrate why we should once and for all settle this matter and have a stable peace." He did not elaborate.

The first question at the news conference, the third Reagan has held since taking office, dealt with a statement he made at his Notre Dame Commencement speech last month when he said that "Western civilization will transcend communism," which he referred to as "a sad, bizarre chapter in human history whose last pages are even now being written." Reagan was asked whether he related this to Poland. He replied:

". . . I think the things we're seeing, not only in Poland, but the reports that are beginning to come out of Russia itself about the younger generation and its resistance to long-time government controls, is an indication that communism is an aberration, it's not a normal way of living for human beings, and I think we are seeing the first cracks, the beginning of the end," Reagan said.

Reagan also was asked why he had not made a major foreign policy speech, as has been suggested to him by some of his aides. The aides proposed that he make the address at the commencement exercises at both Notre Dame and the U.S. Military Academy. Reagan rejected the idea.

Reagan in response detailed a number of foreign policy meetings between members of his administration and various foreign leaders.

"I don't necessarily believe that you must, to have a foreign policy, stand up and make a wide declaration that this is your foreign policy," he said.