After weeks of alarms about Libyan plans to assassinate President Reagan, U.S. analysts with access to the latest top-secret intelligence now say the alleged Libyan hit squads --two of them, with five members each--have suspended their operations, at least temporarily.

This supposed suspension of their activities can only add to the question marks that continue to hang over the whole episode.

Reagan has said he has evidence that hit men under Libyan strongman Muammar Qaddafi threaten U.S. leaders. The administration has not made that evidence public. Nor has it made public its basis for saying now that the squads have suspended operations.

This has compounded the shadowy nature of the affair, confronting the public with diametrically opposite assertions by rival governments set forth in newspaper headlines.

The administration and Qaddafi have been hammering at each other in public almost all year. The assassination plot is the most serious accusation that has been made against his regime.

Sources say there is debate within the administration now as to why the hit squads have become inactive and how long Qaddafi will keep the alleged assassination plots on hold.

One theory within the government is that the bright glare of publicity and U.S. denunciations caused Qaddafi to have second thoughts about going ahead with the idea. However, high-level sources continued to insist that the assassination threat was real.

The U.S. government had hard evidence, sources said, that two multinational five-man hit squads had indeed been trained in how to assassinate the American president. East German terror experts helped in the training, officials said.

The source for this hard evidence is the most closely guarded secret of all within the Reagan administration. Unconfirmed press reports said the information came from an informant whose credibility was tested and passed muster.

However, the information about the hit squads beyond their training has been and still is mushy, sources said. The United States still does not know for sure whether any members of the two hit squads ever left Libya, for example, sources said.

Also, intelligence reports of assassination threats against American presidents by foreign operatives are nothing new. But this time Reagan and other top officials took the unusual step of publicly discussing the threat and declaring they had evidence it was real.

"Once you learn about a threat to the president's life," said one government specialist, "you'd be crazy not to take it seriously. But we've had lots of them that nobody talked about."

The specialist's view on assassination attempts helps explain why two government officials with access to the same secret information can give different assessments without really contradicting each other in the technical sense.

Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) told reporters on Dec. 16 that "the risk is diminished some." White House communications director David Gergen, in response to Baker's comment, said, "I know of no reason to believe the threat has diminished."

A non-government publication specializing in Middle East events, The Middle East Policy Survey, reported recently that the Central Intelligence Agency "now believes that Libya's Col. Qaddafi ordered the recall of the hit squad before it reached the United States."

Two congressional sources who heard CIA briefings on the Libyan hit squads said that the agency at no time asserted it had evidence that any of the suspected assassins had left Libya or any other launching point and had arrived in the United States.

Members of the House and Senate briefed by the CIA acknowledged that there were grounds to be concerned about the threat of assassination to the president and other high government officials. Several interviewed said they felt the portrayal of the threat had been exaggerated by both the media and the Reagan administration. One House member said the threat from Libyan hit squads did not seem to him to be any more serious than other ones the White House learns about on an almost daily basis.

On Dec. 7, Reagan told reporters that "we have the evidence" that Qaddafi planned to try to assassinate U.S. leaders. The previous day Qaddafi had dismissed the charge, declaring Reagan was "a liar" for issuing such "silly" reports about assassination.

Indications that the administration really did take the threat seriously showed up in other highly visible ways, such as the posting of extra guards around Reagan and installing them as well for the first time on the third floor of the Pentagon outside the office of Defense Secretary Caspar W. Weinberger.

Still unknown to the U.S. government, and a continuing source of concern, officials said, is what Qaddaffi will do with his freshly trained hit teams.