TOKYO — As the bodies of the seven sailors who died aboard the destroyer Fitzgerald last weekend were flown back to the United States from Japan Tuesday, multiple investigations of the fatal collision with a container ship began in earnest.

The Navy and Coast Guard are investigating, as are the Japanese Coast Guard and the Japan Transport Safety Board, in an effort to determine what caused the crash in a busy sea lane in the middle of the night.

Japanese officials said on Monday that the accident had occurred nearly an hour earlier than previously believed, and on Tuesday the US Navy appeared to accept the revised timeline.

The ACX Crystal, the Philippine-registered ship that collided with the Fitzgerald off Japan, docked in Yokohama on Monday so that its cargo of household goods and machine parts could be unloaded.

The ship left Yokohama Tuesday, but Ryota Kowata, a spokesman for Nippon Yusen, the shipping company that chartered the Crystal, declined to say where it was going. He said that a company that had surveyed the damage to the container ship, to determine whether it was still fit, had ordered it not to leave Tokyo Bay.

It was not clear how long the Crystal and its 20 crew members, all from the Philippines, would stay in Japanese waters. The Japanese Coast Guard declined to comment.

Investigators were expected to want to interview the Crystal’s crew to ask, among other things, why there was nearly an hour’s delay in reporting the crash. The Crystal reported the collision at 2:25 a.m. on Saturday, but Nippon Yusen determined that it occurred around 1:30 a.m.

Junichi Kanegae, a board member of the Japan Captains’ Association, said the crew of the Crystal probably would have reported to the captain and contacted the Fitzgerald before reporting the incident to the Japanese Coast Guard. “It might be possible that the time had passed while the crew was responding on these matters,’’ Kanegae said.

The Crystal, which carried 1,080 containers, left the Port of Nagoya, about 160 miles southwest of the capital, at 4:45 p.m. last Friday on its way to the Port of Tokyo. The collision, off the coast of Shimoda, about 80 miles southwest of Tokyo, inflicted serious damage to the destroyer, causing a section in its middle to cave in, above and below the water line, flooding berths, a machinery area, and the radio room.

The Fitzgerald had recently participated in exercises with two US aircraft carriers and ships from the Japanese Maritime Self-Defense Force. Three Fitzgerald crew members, including its commander, Bryce Benson, were airlifted from the destroyer with injuries on Saturday. All were reportedly released from the naval hospital by Monday evening.