A U.S. Navy ship apparently carrying nuclear weapons remained off the coast of Japan into the mid-1960s, at least three years after senior officials in the Kennedy administration have said they understood the Pentagon had ordered it to stay clear of Japanese territory.

The USS San Joaquin County, an LST (landing ship, tank), remained 100 to 200 yards offshore from the Marine air base at Iwakuni through 1964 and perhaps later, according to two officers who were stationed on the ship.

The presence of a vessel with a cargo of neclear weapons violated a mutual security treaty that forbade the United States to deploy nuclear weapons in Japanese territory.

A political furor in Japan that could endanger the government of Prime Minister Zenko Suzuki was created last month when former U.S. Ambassador to Japan Edwin O. Reischauer revealed that U.S. aircraft carriers and other warships had nuclear weapons aboard over a 20-year period when they entered Japanese ports for route rest-and-recreation and other brief stopovers.

Two weeks ago, the Washington Post disclosed the permanent stationing of the San Joaquin County off Iwakuni starting no later than 1959. This was the first report that nuclear weapons were kept constantly in Japanese territory.

At the time, two former senior officials in the Kennedy administration, Paul H. Nitze, who was assistant secretary of defense for international security affairs, and U. Alexis Johnson, who was deputy under secretary of state for policial affairs, confirmed that the LST had been anchored off Iwakuni into 1961, as asserted in a memo written 10 years later by Daniel Ellsberg, a former Department of Defense specialist on nuclear command and control systems.

But both men recalled to a reporter that when informed in 1961 of the ship's assignment, which reportedly had been concealed from the administration, the Pentagon ordered it to remain in Okinawa where it was undergoing repairs.

A different account was provided by Michael O'Harro, who was the communications officer aboard the San Joaquin County until November, 1963, two years after the ship had supposedly been ordered away from Japan.

Except for three months in Guam for repairs and a brief stop at Okinawa, the ship ws stationed at Iwakuni during his 11-month tour of duty, O'Harro said. Copies of his orders confirm his assignment to the San Joaquin County and its presence in Iwakuni.

O'Harro, now the operator of a Washington nightclub called Tramp's said he will neither confirm nor deny the existence of nulcear weapons aboard the ship because of a secrecy pledge he signed while in the Navy. But his orders authenticate his top-secret clearance.

"They would not have any top-secret clearance for a normal communications ship," O'Harro said. He remembered that he and his colleagues sometimes made off-duty visits to nearby Hiroshima.

Another former officer, who asked that his name not be used, said he was stationed aboard the San Joaquin County at Iwakuni until May of 1964. He acknowledged the mission of the ship had not changed since its arrival at least five years earlier. The officer, now retired from active duty, said he learned in a recent conversation with another former officer who served on the ship that it did not depart Iwakuni until 1966 or 1967.

In addition, he said that the ship's crew knew it carried nuclear weapons in violation of an international agreement between Japan and the United States. v

"But you're in the gung-ho mode," the former officer recalled. "You were there for motherhood and apple pie. You didn't think in terms of what possible repercussions it might have. It just escapes you -- you're just doing your job."

A U.S. Navy spokesman said the Navy neither confirms nor denies the existence of nuclear weapons at any location.

The disclosure about the LST two weeks ago arose from the 1971 memo, which was provided to The Washington Post by Ellsberg.

The memo, dictated by Ellsberg in 1971, said that the LST "had the cover mission of being an electronic repair ship." He also charged that the Navy had deceived responsible Pentagon officials into believing that the ship was assigned to and remained in Okinawa.

In 1961, according to the memo, Ellsberg notified Nitze of his discovery that the LST actually was permanently anchored off Iwakuni. By contrast, Johnson recalled having been alerted by the U.S. embassy in Japan.

According to Ellsberg's account, Nitze prepared a recommendation for Defense Secretary Robert S. McNamara to order the ship to remain in Okinawa. He wrote that McNamara signed such an order but withdrew it to avoid a quarrel with the Navy. Nitze and Johnson recalled, however, that the ship was given the order promptly.

McNamara, outgoing president of the World Bank, has not returned reporters' calls on the subject.