Before the bodies were found, five Japanese Coast Guard ships spent the day scouring the waters off Japan and a U.S. Poseidon aircraft worked alongside two Japanese maritime helicopters to comb the search area for any sign of the missing sailors.
The Arleigh Burke-class guided-missile destroyer USS Fitzgerald, damaged by colliding with a Philippine-flagged merchant vessel, is seen next to a tugboat (R) off Shimoda, Japan in this photo taken by Kyodo June 17, 2017.
Search crews had to work their way through the extensive damage to the Fitzgerald's starboard side before they found the sailors, the Navy said. They were transferred to a USA naval hospital for identification, it said.
During the collision, a commander and two sailors were injured.
USA investigators are now trying to determine why a warship collided with a merchant vessel, killing seven sailors off the coast of Japan.
Crew members from the destroyer USS Dewey were helping stabilize the damaged USS Fitzgerald after its collision off the coast of Japan before dawn Saturday, leaving seven sailors missing and at least three injured.
The surviving Navy crew valiantly worked to cordon off the areas taking on water.
As search and rescue crews gained access to the spaces that were damaged during the collision on early Sunday morning, the missing sailors were located in the flooded berthing compartments. Bryce Benson, who is reportedly in stable condition after being airlifted to the U.S. Naval Hospital in Yokosuka.
Abe wrote, "I express my heartfelt solidarity to America at this hard time", praising USA servicemen in Japan under the allies' bilateral security pact.
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In an earlier statement, it said that the sailors were being transferred to a U.S. naval hospital where they would be identified.
The other two were being treated for lacerations and bruises.
Because of the hour when the collision happened, many sailors were sleeping, but the ship had a "full complement" of bridge crew on duty, Aucoin said.
Obara said the coast guard was interviewing the crew of the Crystal to determine whether negligent piloting by either side contributed to the collision.
The container ship ACX Crystal weighs 29,060 tons (26,363 tonnes) and is 222 metres long, much larger than the 8,315-ton (7,543-tonne) Navy destroyer.
Adm Aucoin declined to say what might be to blame for the accident, the cause of which is being investigated.
All of the ACX Crystal's 20-member Filipino crew were safe, according to Japanese shipping company Nippon Yusen K.K., which operates the ship.
Minimal damage can be seen at the front of the ACX Crystal.
It's unclear what caused the collision, which occurred about 2:20 a.m. local time, between the destroyer and the container ship that is about four times its size.