The leaking of secret cables describing conversations between Sen. Charles Percy (R.Ill.) and top Soviet leaders -- a revelation that may have been meant to embarrass Percy -- has wound up causing a major embarrassment to the transition team of President-elect Ronald Reagan and a crackdown on security in the Reagan camp.

The controversy was triggered yesterday when The New York Times published portions of messages to the State Department from Thomas J. Watson, U.S. ambassador in Moscow. Those messages said that when Percey visited Moscow two weeks ago he told Soviet leaders he favored creation of a Palestinian state headed by Yassar Arafat, leader of the Palestine Liberation Organization -- an idea that is vehemently opposed by Israel and is at odds with Reagan's position.

The Watson messages, according to the article, also portrayed the Soviets as apparently telling Percy they were unwilling to reopen negotiations on the strategic arms limitation treaty (Salt II). That appeared to be at odds with Percy's public statements of optimism about reopening talks on the stalled arms treaty.

Percy, who is slated to become chairman of the Senate Foreign Relations Committee in the new Republican-controlled Senate, is a moderate whose foreign policy views frequently are more in accord with those of Democrats than conservative Republicans. His trip to Moscow, coming just two weeks after the election, is known to have annoyed many hard-line Republicans, concerned that his views would be regarded as reflecting the attitudes of the Reagan administration.

The leaking of the classified cables, however, has serious implications beyond the substance of Percy's views. Top officials of the Reagan transition group said it is essential that foreign governments trust their conversations will be kept in confidence. Some of Percy's discussions were with Soviet President Leonid Brezhnev. Other officials, fearing that the leaks reflect "guerrilla warfare" among various factions of the transition group, expressed concern about the effect on the development of new policies.

Yesterday, the leader of the transition group working at the State Department, former ambassador Robert E. Neumann, called in some 15 team officials at a special meeting about the leaked cables and warned of the implications. Reagan's top national security adviser, Richard V. Allen, attended the meeting, and Allen, other officials said, was spreading the warning about security to other teams working in the Pentagon and elsewhere in government.

Neumann said in a telephone interview that the leaks "don't look good. They endanger the integrity of the transition process." To disagree over policy is one thing, he said, but to leak classified cables is another. "It's dishonorable," he added.

Aside from the transition team, the Watson cables were also said to be available to the members and staff of the Foreign Relations Committee.

One senior transition official said privately he felt the leak was meant primarily to discredit Percy and secondly to stop any more moderate policies from developing.Another said he thought it was primarily an attempt to divide "and make trouble for the transition process, or trouble between the seantor and the incoming administration. If you were trying to make trouble for us," he said, "this is how you would do it."

Another official recalled how, in the early 1970s, hard-liners in the Nixon administration were accused of trying to sabotage the SALT talks with embarrasing leaks about U.S.-Soviet discussions.

Percy was not available for comment yesterday. However, his executive assistant, Scott Cohen, said the material quoted by The Times, while accurate consisted of "very selective segments of cables that took outwardly sensational statements out of context and gave them a misleading and, in some cases, distorted picture of Percy's views." Cohen said the cables were not verbatim transcripts but were paraphrased accounts based on shorthand notes.

Cohen also took exception to a statement in the news article that Percy left Soviet leaders with the implication Reagan favors a Palestinian state.

"The senator did not discuss his Middle East comments with Gov. Reagan before or after his Moscow trip, and he said very explicitly in Moscow that he was speaking about the Middle East in his capacity as a U.S. senator," Cohen said.

Percy's views on the Middle East have been a matter of public record since 1975 and the senator did not deviate from them in Moscow, Cohen said. "The senator has long believed there can be no peace without a solution of the Palestinian problem. It is his view that the Palestinian people should have a territory on the West Bank and in Gaza so long as it is federated with Jordan and is demilitarized for at least 25 years, until they have demonstrated they will live in peace without being a threat to any nation in the region.

"Percy continues to oppose the United States negotiation with the PLO until the PLO recognizes Israel's right to exist as a sovereign state, recognizes the right of the Israeli people to live within defensible borders, renounces terrorism and accepts United Nations Resolutions 242 and 338," Cohen said.

Cohen acknowledged that Percy said if a Palestinian state were established "Arafat or anyone else they elected could be their leader." But Cohen said Percy stressed that such a state would not be an armed and agressive state and that Arafat, or anyone else, would have to accept that.

With respect to SALT, Percy had said before going to Moscow that he had "coordinated" his positions through talks with Allen and other Reagan advisers. Cohen contended that there was no real discrepancy between what the Soviet leaders told Percy in private and the senator's subsequent public statement that he was "relatively optimistic" about negotiations on a substantially revised treaty.

"Percy told them that SALT II is as dead as a doornail," Cohen said, but "it wasn't clear at any point that the Soviets were insisting that they wanted SALT II ratified or nothing. As a result, Percy concluded that the door was still open . . . ," Cohen said.