Government officials said yesterday that an Israeli gunboat raced alongside a cargo ship taking Palestine Liberation Organization combatants from the port of Beirut, lowered its guns as if to blow the ship out of the water, then sped from the scene--in full view of the escorting U.S. destroyer.

The gunboat moved between the evacuation ship, the Santorini, and the destroyer Manley before passing along one side of the Santorini and then the other as the 700 PLO guerrillas on board watched, officials said.

No shots were fired during the brief but tense confrontation just off Beirut as the Israeli gunboat came within 400 yards of the cargo vessel, very close for sea encounters, officials said.

The incident occurred last Thursday but has not been protested by the State Department, which did make a formal objection after an incident Aug. 7 when Israeli fighters buzzed U.S. helicopters.

A State Department official said yesterday that the department knew about last Thursday's instance of Israeli harassment but decided against lodging a formal protest for fear it would snarl the sea evacuation from Lebanon, which otherwise was going smoothly. The department decided to leave it to officials on the scene to object to the harassment, he said.

Military officials, some of whom are complaining because the United States did not file a sharp protest, said the Israeli gunboat that threatened the Santorini had made less menacing passes against another evacuation ship last Tuesday.

A Pentagon spokesman said last night that reports from ships on the scene did not identify the Israeli gunboat, perhaps because its name, written in Hebrew, could not be understood.

Government officials gave this account of the encounter Thursday:

The Santorini, a Greek ship chartered by the International Committee of the Red Cross, had cleared Beirut harbor and was steaming at about 15 knots. The Manley, a 25-year-old warship with a crew of about 300, maneuvered to take up an escorting position astern of the Santorini.

Before the Manley was in position, an Israeli gunboat roared from the port area and overtook the Santorini. The gunboat ran along the starboard side, crossed the bow and turned to run slowly along the port side.

In that position and before moving off, the gunboat lowered its 76-mm guns, training them on the Santorini and locking the guns' radar onto the freighter as if about to fire.

The gunboat was said to be armed with Gabriel and Harpoon antiship missiles as well as the deck guns. Such armament is carried by Israeli fast attack boats of the Saar class.

Israeli planes and ground troops harassed American military personnel planning the PLO evacuation in separate incidents Aug. 7 and 8.

In the first encounter, two Israeli F16 fighters buzzed two U.S. helicopters carrying planners from a meeting with U.S. special envoy Philip C. Habib in Juniyah, Lebanon, to the aircraft carrier Forrestal off the Lebanese coast.

In the second incident, Israeli troops refused to let the six-man planning team go from the helicopter landing area to Habib's residence until they supplied full identification. The Israelis also drove vehicles into the landing zone to keep the helicopters from landing when they returned to pick up the Americans.

The State Department said afterward that the incidents were "of great concern to us," adding that "strong protests" had been made to the Israeli government. State said Israel had assured the administration that "there will be no further actions of this kind."

An Israeli Embassy spokesman said last night that officials here were unaware of the gunboat incident and would have no immediate comment.