The deletion of six little words from the official testimony given to the Senate Foreign Relations Committee last July by William E. Schaufele Jr. has triggered doubt and fear in the government of Greek Prime Minister Constantine Karamanlis over U.S. intentions in the Aegean Sea.

This unreported event must be perceived in the light of a new phase-out of World Bank aid and a cutback of grant military aid for Greece. Both of these are viewed by the strong pro-Greek congressional lobby as pressure on Greece to show flexibility in its dispute with Turkey over control of the Aegean Sea's continental shelf and air space.

What disturbs Greece's allies here is the political effect on Karamanlis, severely weakened in last November's election, and on President Carter's uphill fight to restore the integrity and strength of NATO's southern flank.

It was on July 12 that Schaufele was questioned on his appointment as ambassador to Greece. Until now, the withdrawal of Schaufele's name for that post has been attributed to Greek anger over his use of the phrase "unusual, I must admit, arrangements" governing Greece's sovereignty over Aegean islands near the coast of Turkey.

In fact, however, Schaufele (since named ambassador to Poland) was ruled unacceptable by the Karamanlis government not by those words. What triggered Karamanlis's wrath was deletion of the italicized words in the following State Department "correction" of Schaufele's testimony on ownership of the Aegean islands: "This ownership is based on longstanding international agreements which the United States fully supports."

Shortly after that correction for the official record had been submitted to the Foreign Relations Committee, the State Department ordered the italicized words deleted, a fact discovered by Elias Demetracopoulos and quickly transmitted to Athens. Demetracopoulos, a Greek expatriate and former Athens newspaperman, is best known for his opposition to the former Greek military dictatorship.

U.S. officials vehemently deny any U.S. intention or long-range consideration of any sort for reopening the 1923 Lausanne Treaty, which gave Greece ownership of the offshore islands. Indeed, not even Turkey has questioned the treaty. But the result of the deletion of that phrase - "which the United States fully supports" - caused anguish in Athens, raising the obvious question of why the phrase was struck unless there is at least some future intention of tampering with the treaty.

That a government led by as sophisticated a prime minister as Kramanlis should be traumatized by what may conceivably have been no more than middle-level bureaucratic stupidity at State shows the delicacy of the Greek-Turkish dispute - and the overwhelming influence on it of U.S. policy.

Thus, within days of the unannounced correction, top-level conversations were taking place within the Greek government on the "extremely dangerous" implications of any future change in the Lausanne Treaty. The chamber of horrors exposed by these conversations was what really persuaded Karamanlis to refuse to accept Schaufele as ambassador (an inalienable right of any government).

Starting with the horror of Turkish pressure on the offshore islands, these include long-standing Bulgarian demands for an outlet of its own to the Aegean Sea across a narrow strip of territory now held by Turkey. Any juridical change in the Aegean Sea would automatically open up this demand, with the Soviet Union standing to gain a Warsaw Pact outlet to the Mediterranean, bypassing the Dardanelles.

To Carter adminstration diplomats, Greek preoccupation with such future hobgoblins may be patently ridiculous, but Karamanlis believes the hobgoblins could materialize. On Aug. 19, 1976, then-Prime Minister Demirel of Turkey referred to the disputed islands this way: "They are not Greek islands. Do not call them this way. You should say Aegean Islands."

Karamanlis immediately accused Demirel of "demogogic and contradictory statements." The Greek prime minister's private reaction to the deletion of those of six little words by the State Department is not very different.