One of the biggest bombshells in the Daniel Elsberg's new book, The Doomsday Machine, was that the U.S. stored significant numbers of nuclear weapons on a ship anchored off the coast of Japan near the Iwakuni Base for decades.

“However, in early 1960 I was told in great secrecy by a nuclear control officer in the Pacific that one small Marine air base at Iwakuni in Japan had a secret arrangement whereby its handful of planes with general war missions would get their nuclear weapons very quickly in the event of a general war alert. In contrast to all the other planes on Japanese bases, the Marines at Iwakuni would have nuclear weapons within minutes instead of hours. Because of the special relation of the Marines to the Navy, there was a flat-bottomed ship for landing tanks on a beach (LST, for Landing Ship, Tank), anchored just offshore Iwakuni with nuclear weapons aboard, loaded onto amphibious tractors, just for the small group of planes on this base.
This LST, the USS San Joaquin County, had a cover mission as an electronics repair ship. It was permanently stationed not just inside the three-mile limit of Japanese territorial waters but anchored a couple of hundred yards from the beach, in the tidal waters. By any standards it was stationed within the territory of Japan. And so were its nuclear weapons.”

Excerpt From: Daniel Ellsberg, The Doomsday Machine