Charges that Cyprus' president, Archbishop Makarios, has received money from the CIA have had little impact here because most Greek Cypriots appear to believe that the CIA has been trying to kill Makarios, not subsidize him.

The issue therefore is unlikely to complicate the diplomatic mission of presidential envoy Clark Clifford, who arrived here today on the last leg of an Aegean swing and who lunches with the Cypriot leader on Thursday.

Makarios is standing by his denial of American newspaper allegations that the received any money, but it appears unlikely that he will pursue seriously threats by his supporters that he would sue The Washington Post - and thereby risk publicity about some quiet U.S. activities in Cyprus.

It is an article of faith here that the prickly leader was the target of four assassination attempts by the CIA since 1970, culmination in the 1974 coup launches by the rightist EOKAB group in collusion with the anti-Makarios junta then in power in Greece. The junta had close links with the CIA and such links with the EOKA-B have been authoritatively reported in the past.

Greek Cypriot opinion is ill prepared to envisage the paradox of the CIA simultaneously trying to eliminate Makarios and supporting him after the late 1960s. He had emerged then as a determined antagonist of the Turkish Cypriots and Turkey, who enjoyed American support. In some American circles he was labeled "the Castro of the Meditteranean," and the blatant hostility toward Makarios of the CIA station chief here from 1969 to 1971 was noticed by diplomats.

Makarios definitely was an obstacle to any absorption of Cyprus into NATO, which many Greek Cypriots believe was a U.S. foreign policy objective.

At the same time, Makarios allowed Cyprus to be used as a base for some covert operations by both blocs. The archbishop, described as a man of conservative temperament by his intimates, held the line against any bid for power by the Communists, who traditionally control 40 per cent of the votes.

Skepticism about the reported CIA payments to Makarios could change if detailed corroboration surfaced, but there has been no local confirmation.

The allegations have been fully reprinted in the Greek Cypriot newspapers alongside Makarios' denial and his challenge to his accusers to produce proof.

Even his leftist critics have shied from trying to make political capital during the present crucial bargaining over the island's future. Newspapers in the Turkish Cypriot zone and in mainland Turkey reprinted the charges without comment. Turkish propaganda has often charged that Makarios is a dangerous anti-NATO radical.

So far, the widespread faith in Makarios here has been reinforced by his dismissal of the charges and the hints emanating from the highest officials and discussed in a newspaper here that Makarios is considering legal action against The Washington Post.

The only skeptics are a handful of diplomats who refuse to rule out the possibility that Makarios, like other Third World leaders in the 1960s, took funds from Washington while letting his local rivals take handouts from the Communist bloc - all ultimately for the enrichment of Cyprus.

Despite his self-confident tone, Makarios probably will avoid going into court, observers here feel, because a lawsuit would spotlight many semicovert American operations on this island, strategically located in the eastern Mediterranean.

The Makarios government has avoided publicizing these facilities locally. The best known is the radio monitoring operating run here by the Foreign Broadcast Information Service - a CIA budgeted service that records and translates the broadcasts of every audible station in the Middle East. Its product, which is shared with the British Broadcasting Corp., is available in the United States and abroad through the Department of Commerce.

Unlike the British equivalent (and now partner), FBIS is funded from intelligence funds.

The United States made an agreement in 1968 for the FBIS facilities and for a State Department radio relay operation here. While the official "stations agreement" is still operative and is publicly known, the amount of annual rent is confidential. Authoritative sources here say it is slightly more than $1 million annually.

The sums and dates correspond with the reported payments to Makarios, but these funds are a properly accounted government-to-government payment.

The key question is whether a second, separate set of paymnets was made to Makarios personally beyond the governmental compensation for the facility.

For instance, Makarios' discretion might have been essential if the FBIS facility were used in National Security Agency operations - a combination that has been alleged by ex-CIA agent Philip Agee and Journalist Mark Hosenball.

Ex-CIA operatives in the past have described American plans to use Cyprus-based radios for "blacks" propaganda [which gives the impression it is issued by the other side] and military monitoring in the Middle East - an embarrassing disclosure, if proven, for Makarios' friendship with the Soviet Union and Arab governments. The FBI operation, formerly located near Kyrenia, was moved south to Nicosia and scaled down after the Turkish invasion of Northern Cyprus in 1974.

A less sensitive point, on which the Makarios government was also obliging, was the staging of U.S. U-2s from an airbase on Cyprus since 1967. The spy planes used the British base Akrotiri in southern Cyprus for armistice supervision in Sinai in 1967 and again after the 1975 Egyptian-Israeli disengagement accord - and perhaps for other missions.

While Akrotiri is a sovereign British base over which Makarios legally has no veto, it would nonetheless be important to secure the Archbishop blessing. This cooperation could be presented among Cyprus' small political leadership as relatively harmless, but Markario has never sought to explain it to Cypriot public opinion.