Bodies of missing sailors have been found in the flooded berthing compartments of the U.S. Navy destroyer USS Fitzgerald, one day after it collided with a merchant ship off the Japanese coast, the U.S. Navy said in a statement on Saturday.

The remains were transferred to Naval Hospital Yokosuka where they will be identified, the Navy said.

Vice Admiral Joseph Aucoin, commander of the 7th Fleet, said they would not say how many bodies were found until after all the families were notified.

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As of 2 p.m. local time on Sunday, Aucoin said they had discontinued search and rescue.

The Fitzgerald was struck by the Philippine-registered container ship ACX Crystal. The Philippine ship is 29,060 tons and 730 long, the coast guard said, much larger than the 8,315-ton naval destroyer. Aucoin said most of the damage could not be seen because it was below the water line, including a large gash.

"The damage was significant -- this was not a small collision," Aucoin said. "It was extensive damage."

Aucoin said he was "really proud" of the crew for keeping the ship afloat.

Aucoin said he would oversee a "thorough investigation" into what caused the collision, but he wouldn't speculate on what happened. He said he couldn't speculate on how long the investigation will take.

The area is particularly busy with sea traffic, said Yutaka Saito of the Coast Guard.

Japanese vessels first arrived on the scene and the coast guard is leading the search. U.S. aircraft is assisting in the effort, along with several Japanese helicopters and one plane, the 7th Fleet said.

The collision injured the vessel "above and below the water line, causing significant damage," the 7th Fleet said.

The Fitzgerald, an Arleigh Burke-class guided missile destroyer commissioned in 1995, is based in Yokosuka, according to the Navy. Its crew typically includes 23 officers, 24 chief petty officers and 291 enlisted sailors.

The Fitzgerald's captain, Cmdr. Bryce Benson, was airlifted to the U.S. Naval Hospital in Yokosuka and was in stable condition, the 7th Fleet said in a statement. His cabin was destroyed, Aucoin said. "He's lucky to be alive," Aucoin said.

Two other sailors with minor injuries were also medevaced, Aucoin said. It was unclear how many others may have been hurt.

The Fitzgerald had limited propulsion after suffering damage on the right side below the water line and a U.S. defense official said there was flooding in three compartments. It wasn't clear yet what caused the nighttime collision between the destroyer and the container ship four times its size. Most of the more than 200 sailors aboard would have been asleep in their berths, some of which were reportedly flooded.

Despite the "extensive" damage, Aucoin vowed the USS Fitzgerald would return.