ATHENS, Greece (AP) _ For the second time since June, Athens airport has been linked to a jet hijacking in which passengers have died. But Greek officials, who insist the airport is safe, say the sky pirates smuggled their weapons aboard elsewhere.

An Egyptair jet was commandeered Saturday after leaving Athens on a flight to Cairo, Egypt. The Boeing 737 flew to Malta, where Egyptian commandos stormed it, leading to a bloodbath in which up to 50 people were killed and 28 hospitalized for injuries.

On June 14, a TWA flight departing from Athens for Rome was also seized by terrorists. One passenger, U.S. Navy diver Robert Dean Stethem, 23, of Waldorf, Md., was shot dead during the ordeal.

In both cases, Greek officials have countered criticism by saying the weapons used might have been put on board in Cairo before the planes arrived in Athens.

Under fire from British legislators and the French National Airlines Pilots Union, which called for a boycott of Athens airport because of a ''certain laxity,'' the Greek government on Sunday said security was ''exercised with the highest international standards.''

Quoting ''heads of security,'' the government announcement maintained that the weapons used to hijack the Egyptair Boeing 737 were probably hidden aboard the plane in Cairo before it flew to Athens to pick up passengers and return.

However, an Egyptian Embassy spokesman said, ''Obviously, the hijackers boarded in Athens.'' He spoke on condition he not be identified.

Passengers released by the hijackers in Valletta, Malta, said they were carrying small arms and at least one hand grenade. In radio conversations, they had identified themselves as belonging to the group ''Egypt's Revolutionaries,'' which has opposed Egypt's 1979 peace treaty with Israel$

The Greek Civil Aviation Authority said passengers boarding at Athens were subject to five checks, including examination by a ''special security firm'' employed by Egyptair and electronic devices operated by Greek police to perform body checks of passengers.

Greece also insisted that weapons used by hijackers to commandeer the TWA jetliner after it left Athens in June were hidden aboard the aircraft in Cairo. But one of the accomplices who was later arrested, Ali Atwa, said the weapons had been smuggled aboard the plane in Athens.

The Shiite Moslem hijackers of the Trans World Airlines plane, which had 153 people on board and ended up in Beirut, held 39 Americans hostage for 17 days. They were demanding the release of Palestinian and Lebanese prisoners held in Israel.

In response to the TWA incident, the State Department issued a travel advisory on June 18 warning Americans to avoid Athens airport.

As a result, many Americans canceled vacations in Greece, causing millions of dollars in lost tourist revenue.

The travel advisory was lifted July 22 after stringent airport inspections by the International Air Transport Association and the Federal Aviation Administration.

Both air groups praised the new security measures put into effect after the hijacking and described Athens airport as ''probably one of the world's best guarded airports.''

The TWA hijacking prompted Greek officials to adopt new security measures, especially in the airport transit area.

Police double-checked hand luggage after it passed through X-ray machines and restricted movement between the departure and arrival halls by closing off many exits.

Many international airlines also employ their own security guards.

Egyptair passengers departing for Cairo Sunday reported that Egyptian air marshals conducted body searches of everyone who boarded the plane, and scrutinized their hand luggage.

But Western diplomats in Athens, insisting on anonymity, say security problems persist at Athens airport, and cite what they say is a poor security fence on the airport perimeter as a major problem.

Police say the perimeter is being heavily patrolled, pending completion of a new high-security fence later this year.

But in April, a gunman got close enough to the runways to fire an anti-tank rocket at a Jordanian passenger jet as it prepared for takeoff. The missle hit the plane, but failed to explode.