The bodies of sailors missing since the destroyer the USS Fitzgerald collided with a container vessel were found in flooded compartments in the damaged ship, the United States Navy said on Sunday.

"As search and rescue crews gained access to the spaces that were damaged during the collision this morning, the missing sailors were located," the U.S. Seventh Fleet said in a statement.

The statement did not say if all seven missing crew members were found in the ship, however Japanese media reported that all seven had been found dead.

However, a later statement from the navy said not all the bodies were recovered. 

Most of the nearly 300 sailors aboard would have been asleep in their berths at the time of the collision. Two berthing spaces, a machinery room and the radio room were damaged and began taking in water after the destroyer was rammed mid-right side of the ship. 

Those who did not survive might have been killed by the impact of the crash or drowned by the flooding, said Navy spokesman Lieut. Paul Newell, who led reporters for a first look at the mangled vessel.  

The U.S. Navy destroyer arrived at its base in Yokosuka early Saturday after it collided with a Philippine-flagged container ship more than three times its size in eastern Japan.

The Fitzgerald, an Aegis guided missile destroyer, collided with the merchant vessel at about 2:30 a.m. local time, some 56 nautical miles (103 kilometres) southwest of Yokosuka, the Navy said.

Three aboard the destroyer had been medically evacuated to the U.S. Naval Hospital in Yokosuka, including the ship's commanding officer, Cmdr. Bryce Benson, who was reported to be in stable condition, the Navy said. The other two were being treated for lacerations and bruises, while other injured were being assessed aboard the ship, it said.

Search and rescue efforts by U.S. and Japanese aircraft and surface vessels were continuing for the seven missing sailors, the Navy said. Their names are being withheld until the families have been notified, it said.

Benson took command of the Fitzgerald on May 13. He had previously commanded a minesweeper based in Sasebo in western Japan.

Unclear what happened

It was unclear how the collision happened. "Once an investigation is complete then any legal issues can be addressed," the 7th Fleet spokesman said.

The Fitzgerald suffered damage on her starboard side above and below the waterline, causing "significant damage" and flooding to two berthing spaces and other areas of the ship, the Navy said. The flooding was later stabilized, but it was uncertain how long it would take to gain access to those spaces once the ship is docked, to continue the search for the missing, it said.

AFP_PM7Q3

Seven U.S. sailors remain missing after the guided missile destroyer collided with a container ship off the coast of Japan. (STR/AFP/Getty Images)

The ship was able to operate under its own power with limited propulsion, the Navy said. The Japanese Coast Guard said separately the Fitzgerald was towed back to Yokosuka by a tugboat at about 3 knots.

Vessel underwent recent upgrades 

Part of an eight-ship squadron based in Yokosuka, the Fitzgerald had in February completed $21 million US worth of upgrades and repairs.

Japan's Nippon Yusen KK, which charters the container ship, ACX Crystal, said in a statement it would "cooperate fully" with the Coast Guard's investigation of the incident. At around 29,000 tons displacement, the ship is far heavier than the 8,315-ton U.S. warship, and was carrying 1,080 containers from the port of Nagoya to Tokyo.

Bryce Benson

Cmdr. Bryce Benson was taken to the U.S. Naval Hospital in Yokosuka and was in stable condition, the U.S. 7th Fleet said in a statement. (U.S. Navy)

None of the 20 crew members aboard the container ship, all Filipino, were injured, and the ship was not leaking oil, Nippon Yusen said. The ship arrived at Tokyo Bay around 5 p.m. (0800 GMT), sailing under its own power, the Coast Guard said.

The Japanese shipping company said in a statement it is collaborating with the ship owner and fully co-operating with the investigation. 

Japan's Kyodo News service says the Japanese coast guard is investigating the accident and plans to question the crew members of the ACX Crystal.

The cause of the collision wasn't immediately clear.

The waterways approaching Tokyo Bay are busy with commercial vessels sailing to and from Japan's two biggest container ports in Tokyo and Yokohama.

Japan's public broadcaster NHK showed aerial footage of the Fitzgerald, which had a large dent on its right, or starboard, side. Images broadcast by NHK showed it had been struck next to its Aegis radar arrays behind the vertical launch tubes.

Such incidents are rare.

In May, the U.S. Navy's USS Lake Champlain collided with a South Korean fishing vessel but both ships were able to operate under their own power.

The 7th Fleet commander, Vice Admiral Joseph Aucoin, thanked the Japanese Coast guard in a post on the fleet's Facebook page, adding: "We are committed to ensuring the safe return of the ship to port in Yokosuka."

With files from The Associated Press