The crew were reported missing after Saturday's predawn collision, triggering a major US-Japanese search operation, with divers scouring damaged areas of the destroyer.
Yesterday, US authorities tacitly acknowledged there were no survivors as they ended the search, but declined to say how many bodies had been found until the families were notified.
The 154-metre (500-foot) Fitzgerald -- commissioned in 1995 and deployed in the Iraq war in 2003 -- was pulled by a tugboat back to its base on Saturday in Yokosuka, southwest of Tokyo.
"The remains of seven sailors previously reported missing were located in flooded berthing compartments, after divers gained access to the spaces," it said, adding that the deceased sailors ranged in age from 19 to 37.
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Several other US crew members were injured in the accident and had to be evacuated by air to hospital, including the vessel's commanding officer Bryce Benson.
The accident happened 56 nautical miles (104 kilometres) southwest of Yokosuka, in a busy shipping channel that is a gateway to major container ports in Tokyo and nearby Yokohama.
The container ship, the 222-metre Philippine-flagged ACX Crystal, came into port with large scrapes on its bow, but none of its 20 crew were injured, Japan's coastguard said.
The accident is under investigation.