In a brief written statement, the U.S. Pacific Fleet in Hawaii said the Navy requested assistance from the Japanese Coast Guard. A news release from U.S. Seventh Fleet confirmed that two berthing spaces, an auxiliary machine room and the ship's radio room all flooded.
"The families are being notified and being provided the support they need during this hard time", the Navy said.
Aucoin said 116 crew members were in two berthing rooms, a lot of them likely resting at the time of the collision.
The early Saturday morning collision with a Philippines-flagged merchant ship caused extensive damage to the USS Fitzgerald, a guided-missile destroyer, and left seven of its crew members unaccounted for.
"The search and rescue is over", United States 7th Fleet commander Vice Admiral Joseph Aucoin told reporters, describing huge amounts of water that gushed into the sleeping compartments after part of the ship's right side caved in.
Sykes says her son told her that sailors initially believed they were under attack and some immediately went to man the guns. "Now that the ship is in Yokosuka, I ask that you help the families by maintaining their privacy as we continue the search for our shipmates", he said before the announcement that the bodies were found.
The boat returned safely to its home port of Yokosuka, Japan on Saturday night, ending its 17-hour ordeal. Navy spokesman Lt. Paul Newell said the victims may have been killed by the impact of the collision or drowned in the flooding.
Japanese media said all seven of the sailors who had been reported missing were found dead. "The damage was significant", he said. The two damaged berthing compartments house a combined 116 crew members, Aucoin said.
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Three people were medically evacuated to the US Naval Hospital in Yokosuka after the collision, including the ship's commanding officer, Commander Bryce Benson, who was reported to be in stable condition.
The Navy said the dead United States crew were found by the divers. US aircraft is assisting in the effort, along with several Japanese helicopters and one plane, the 7th Fleet said.The area is particularly busy with sea traffic, said Yutaka Saito of the coast guard.
"You will see the USS Fitzgerald back", Aucoin said.
"The incident is now under investigation", the statement said.
The ACX Crystal weighs 29,060 tons and is 730 feet long, the coast guard said, much larger than the 8,315-ton Navy destroyer.
Japan's public broadcaster NHK showed aerial footage of the destroyer, which had a large dent in its right, or starboard, side.
Minimal damage can be seen at the front of the ACX Crystal.
The container ship was seen making a U-turn before the collision on some ship trackers, a move that has raised questions about what happened.