Former secretary of state Henry A. Kissinger conferred secretly with a senior aide to Palestine Liberation Organization Chairman Yasser Arafat in Morocco several months ago in a meeting that has become a complicating factor in the Reagan administration's drive for a Middle East peace settlement.

U.S. officials who confirmed the encounter yesterday vehemently denied that Kissinger had sought to set up a "back channel" with the PLO that would have undercut the Reagan administration's efforts to bring Arafat and Jordan's King Hussein together on a formula allowing Hussein to enter peace negotiations with Israel.

Kissinger, who said that he had met for half an hour with Ahmed Dajani, a member of the PLO's executive committee, in Rabat in late November, also asserted that the meeting with Dajani "had absolutely no political significance. I am not conducting my own foreign policy." Kissinger said he was not aware before the meeting that Dajani was a PLO official.

Other sources report that the meeting was arranged by Morocco's King Hassan II, with the involvement of the U.S. ambassador to Morocco, Joseph Reed, who, like Kissinger, has long been a close associate of New York banker David Rockefeller. A senior State Department official said yesterday he did not know if Reed had played a role in setting up the encounter.

The long delayed talks between Arafat and Hussein on a joint negotiating formula began in Amman last weekend and have reached a critical point, Arab and U.S. sources said yesterday. Arafat is due to return to Amman later this week for a final negotiating session with the Jordanian monarch.

As secretary of state, Kissinger was responsible for the pledge made to Israel in 1975 that the United States would not have formal contacts with the PLO until the Palestinian organization accepts Israel's right to exist and accepts U.N. Resolution 242, which calls for Israel to return territories occupied in the 1967 Arab-Israeli war in return for a peace settlement.

The PLO repeatedly has sought to break through Kissinger's commitment and establish direct contacts with the United States. Qualified sources said that the Kissinger-Dajani meeting appeared to Arafat to hold out hopes that he could achieve that goal without having to make a deal with Hussein, and that the PLO leader began in February a delaying campaign on the negotiations with Hussein. At about the same time, some of his aides began floating the idea that the PLO could negotiate directly with Israel.

The delay was especially troubling for Hussein, who had set March as a deadline for his decision on accepting or rejecting President Reagan's peace initiative. When reports of the meeting in Morocco reached him, Hussein testily demanded an explanation from the Reagan administration, and it was delivered to him in mid-March during a trip to London, according to a number of sources.

Reagan's special Middle East envoy, Ambassador Philip C. Habib, reportedly advised the king that the Reagan administration had nothing to do with the Kissinger-Dajani discussion and denied that the administration was considering modifying its refusal to deal with the PLO.

"Whatever the intention of that meeting, the reports of it and the impression that Kissinger would attempt to set up future meetings that would clear the way for a PLO-U.S. dialogue put a lot of static on the line at a crucial moment," one involved Arab official said. A State Department official agreed that the reports "appeared to put the thing off the tracks for a while."

State Department officials repeatedly emphasized in telephone calls they placed to The Washington Post yesterday that disclosure of the meeting now could affect the delicate negotiations in Amman. The United States and Hussein are known to be resisting Arafat's demands that an agreement be taken to a new Arab summit, to be held in Morocco in mid-April, before any announcement is made.

These officials also emphasized their view that Kissinger had not acted improperly and that he had made a full private report to the administration after the meeting.

Dajani, a writer and historian who lives in Cairo and has served as Arafat's spokesman to the European Community, has been at Arafat's side during the talks in Amman this week, Washington Post correspondent Herbert H. Denton reported from Amman. Asked about his contact with Kissinger, Dajani told Denton, "This is not the time to talk about the Kissinger meeting."

Kissinger arrived in Morocco on Nov. 28 to attend a meeting of the American-Moroccan Foundation, a private organization whose board of trustees he cochairs and of which Rockefeller is chairman of the advisory council. Robert G. Neumann, former Reagan administration ambassador to Saudi Arabia, is chairman of the foundation's executive committee and traveled with Kissinger.

Kissinger asserted in a telephone interview yesterday that he had "no idea of who Dajani was" when he agreed to a request to meet with him "in the social context" of a meeting of King Hassan's Moroccan Academy going on at the same time in Rabat. Kissinger said he thought that Dajani, whom he knew to be a Palestinian, was a member of the academy, which groups Arab intellectuals.

The two men met alone over coffee for about 30 minutes. Kissinger declined to discuss what was said during their talk. He reported its contents to Habib, who was also in Rabat that day, and subsequently to the State Department in writing.

At the time of the meeting with Kissinger, Dajani already had been appointed Arafat's chief delegate on the joint Palestinian-Jordanian commission that worked out the conditions for the negotiations between Arafat and Hussein over the Reagan initiative. The president's proposal, which calls for negotiations to create a Palestinian entity on the West Bank and in the Gaza Strip that would be associated with Jordan, has been rejected by Israel.

Hussein has made it clear that he will not participate in the Reagan initiative without an endorsement from the PLO, which was anointed as the "sole representative" of the Palestinian people by the Arab summit in Rabat in 1974. Arafat has maintained a deliberate ambiguity about the Reagan plan, criticizing its rejection of an independent Palestinian state but saying that it has "positive elements." Although both Secretary of State George P. Shultz and Reagan's national security adviser, William P. Clark, frequently consult Kissinger on the Middle East and other foreign policy questions, State Department officials yesterday emphasized that he is playing no formal role for the administration. Kissinger, who lunched with Shultz yesterday, is due to leave shortly on another private trip to the Middle East.

Lower level U.S. officials said Morocco's King Hassan has avidly sought a middleman's role in bringing the United States and the PLO together in a dialogue and views himself as particularly close to Rockefeller, Reed and Kissinger.

During an interview with French journalists in late January, Hassan said that Kissinger "is the first to kick himself" for barring contacts with the PLO. Kissinger "is no doubt working very hard today" with the U.S. authorities "to try to demolish this negative legend. I have in my possession certain elements that I'm sorry I cannot give you here which buttress my optimism."

"That is not correct," Kissinger said yesterday. "I support our government's policy on this totally."

A senior State Department official supported this assertion and said any suggestion that the Reagan administration had sought to encourage "an alternative channel is absolute fantasy."

Kissinger's secret talks with Chinese, Soviet and other world leaders outside diplomatic channels and without the knowledge of the State Department during the Nixon administration popularized the phrase "back channel" negotiations.