An earlier 7th Fleet statement on Sunday said the sailors had been found and were being transferred to Naval Hospital Yokosuka, but did not state whether they were dead.
The missing sailors' names were being withheld, pending notification of their families.
According to Japan's public broadcaster NHK, all seven bodies of the missing sailors were found aboard the destroyer in areas that had become flooded after the collision, such as a living space and a machine room.
The vessel - which sailed to a Tokyo port Saturday afternoon - is a commercial container ship with a Filipino crew, according to its Japanese owner, NYK Line.
Search crews found the missing sailors after they were able to gain access to parts of the ship that were damaged in the collision.
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In a tweet, the 7th Fleet said the vessel was the Philippine-flagged merchant ship ACX Crystal.
Kyodo news agency, citing the Japanese coast guard, said seven USA crew members were missing.
The 154-metre Fitzgerald is based at Yokosuka, south of Yokohama and Tokyo, and operates in the Pacific and the Sea of Japan.
USA 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. Following the crash, the USA guided missile destroyer suffered "significant damage" above and below the waterline and was partially flooded.
Bryce Benson, were evacuated from the damaged vessel and are being treated at the U.S. naval hospital at Yokosuka, the home of the U.S. Navy's Seventh Fleet.
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The Japanese coast guard said the two ships collided in the dark waters of the Pacific Ocean Saturday around 1:30 a.m. local time - roughly 56 nautical miles southwest from the port of Yokosuka, and 12 miles off the Izu Peninsula, the Washington Post reported.
The ship's commanding officer was among three people aboard to be hospitalised. The collision had resulted in some flooding and damage to the ship's starboard side.
Container ships like the Crystal have bulbous bows under the waterline and that portion of the cargo vessel plowed into the U.S. warship. BBC reports indicate that their ship collided with the vessel about 104km southwest of Yokosuka.
The USS Dewey, medical assistance and two Navy tugs are being dispatched as quickly as possible. Footage showed the damaged ship moving slowly in calm seas, flanked by a tugboat.
The Philippine ship is 29,060 tons and 730 long, the coast guard said, much larger than the 8,315-ton naval destroyer.
The USS Fitzgerald Emergency Family Assistance Center will remain open for chaplain and counselor care indefinitely, 24/7, on the Command Readiness Center's 4th Floor (across from the commissary) - in the same classroom where the Area Orientation Brief (AOB) is hosted.
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