American Jewish leaders rallied behind Israel today in the wake of the government's qualified apology to the United States over the Jonathan Jay Pollard espionage case, saying they considered the matter "closed."

The leaders attended a private breakfast meeting with Israeli Prime Minister Shimon Peres, at which Peres was quoted as saying, "We reached a complete agreement and understanding with the United States; the matter is entirely cleared up."

The leaders of American Jewish organizations who are convening here said they agreed with Peres.

The prime minister, in his public statement of apology last night, had indicated that the Pollard case was far from closed, saying that his government was not yet in possession of all the facts but that the affair would be investigated "no matter where the trail may lead."

Peres, according to U.S. Jewish sources who attended the breakfast, said today that Secretary of State George P. Shultz telephoned him at 3:30 a.m. Israeli time on Sunday with "warm expressions of understanding." That would have been 13 1/2 hours before Peres issued his carefully worded public apology following a Cabinet meeting last night.

The Jewish leaders interviewed said they were not disturbed by what they acknowledged as a long list of unanswered questions surrounding the case. Nor did they feel that Israeli intelligence operatives had jeopardized the standing of the American Jewish community by recruiting, allegedly, a U.S. Jew for a spying mission in his own country.

Among the chief unanswered questions are: whether knowledge of the alleged spying operation reached high levels of the Israeli government; whether it was coordinated with the Israeli Embassy in Washington or was, as claimed by Israeli government officials, part of an unauthorized intelligence network under the direction of a former antiterrorism adviser, and the extent of espionage activities allegedly carried out by a science data-gathering department run by the same man.

Julius Berman, former head of the Conference of Presidents of Major American Jewish Organizations, said here today that it is "obvious" Peres' draft of the apology -- which did not explicitly admit that Israeli-sponsored espionage did take place in Washington -- was coordinated in advance with U.S. officials "to assure that it would be effective."

Berman said the prosecution of Pollard for selling secret U.S. documents to Israel may generate some residual publicity, but "that's just another day or two," then some other big story will come along and the Pollard case will be forgotten.

Howard M. Squadron, another past president of the conference, said, "We live in a television age, and we are so inundated with information that our memories have gotten a lot shorter than they used to be. You can't really recall anything for more than a week."

Other American Jewish leaders said they agreed that the Pollard affair had been buried and that it would have no further impact on U.S.-Israeli relations.

Morris Abram, chairman of the National Conference on Soviet Jewry, said he regarded the Pollard case as "a terrible bungle -- a mistake," and said he is convinced that the controversy will "soon subside."

Peres reportedly told the Jewish leaders: "During the past 24 hours, we have cleared up a great deal of misunderstanding between the United States and Israel, and I am optimistic that we will return to the fine U.S.-Israeli relationship, which has reached new heights in recent months -- a relationship that is important to the United States and the free world."

Peres, according to a conference participant who took detailed notes of the breakfast session, said he objected to "certain hints in the media that a community or a country was spying because in fact it was a single spy which did cause unpleasant occurrences in our midst."

"In a way, it was a test of the strength of our relationship with the United States, and we have passed that test because we have reached this understanding and cleared up the misunderstanding," Peres was quoted as saying.

Kenneth J. Bialkin, the current president of the conference, said in an interview that while spying should not be condoned, "keep in mind that the nature of the secrets obtained does not go to elements of U.S. defense and U.S. preparedness. They touch primarily on elements primarily of Israel's interest to defend itself -- that is, information about the deployment of Arab forces and the nature of Arab strength."

Bialkin added, "Israel is not a nation hostile to the United States, and there is no danger that the kind of information that was obtained in this particular regard will be circuited back to anti-U.S. countries."

He said that "the need for Israel to obtain this kind of information stresses again Israel's circumstance in the world, namely that there is no other nation whose neighbors exist in a declared state of war with an intention to destroy it, and where the imperatives of obtaining information of the type that was obtained are so apparent."

A lesson to be derived from the Pollard affair, Bialkin said, is that "there ought to be an increase in impatience with the rejectionism of the Arab world that creates the sort tensions that put pressure relations between friends."

He added, "The need for Israel to obtain this intelligence is there. Unfortunately, the techniques employed to obtain that intelligence went beyond the policies of the government of Israel, and I would say that you have to be naive in this world to believe that nations will not seek the maximum intelligence available. But in the case of the U.S. and Israel, that has to be done within the framework of the understanding that exists, and I'm not suggesting otherwise."