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

The United States 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 deadly 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 United States Navy appeared to accept the revised timeline. “We’re not disputing what the Japanese Coast Guard is saying” about the timing of the collision, said Cmdr. Bill Clinton, a spokesman for the Seventh Fleet at the American base in Yokosuka, Japan, south of Tokyo.

The ACX Crystal, the 29,000-ton 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.

According to Ryota Kowata, a spokesman for Nippon Yusen, the Japanese shipping company that chartered the Crystal, the ship left the Port of Yokohama on Tuesday, but Mr. Kowata 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 that while that might seem like a long delay, 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,” Mr. 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 American 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.

According to the Seventh Fleet’s Facebook page, all three were released from the naval hospital at Yokosuka by Monday evening.

While the Navy will be conducting an internal investigation of its crew’s operations, the United States Coast Guard, along with its counterpart in Japan, will be trying to determine the cause of the accident.

The Coast Guard, which normally has a small operation of 10 active-duty members at the Yokota air base, has brought in additional investigators from Hawaii and New Orleans.

Lt. Scott Carr, a Coast Guard spokesman, said he could not disclose details of the inquiry, but he said that investigators would typically interview crew members and examine electronic data from the ships involved.

Takahiro Takemoto, professor at Tokyo University of Marine Science and Technology, said investigators would probably have a range of electronic information to examine.

Nautical instruments on large commercial ships track data, and ships usually have a voyage data recorder, or VDR, much like the flight recorders recovered after airplane crashes.

VDRs record conversations on the ship’s bridge as well as other sounds, and track data on the ship’s direction and speed so investigators can reconstruct the course of the ship. It was not clear whether the Fitzgerald had such a device on board.

Professor Takemoto said investigators would also probably look at radar images and electronic charts that would have tracked the ships’ paths.

Ultimately, he said, important information would be gleaned from interviews with the crew members, particularly those who were on night duty.

“How much information we can get from the interviews is the important point to conclude the cause,” he said.