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.
On Sunday, 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 navy said the bodies of the missing crew were found by the divers in flooded sleeping quarters.
"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.
On Sunday, US 7th Fleet commander Vice Admiral Joseph Aucoin said the crew would have had little chance of escaping the "tremendous" amount of water that gushed into the ship after the accident left a large gash in its side.
"It was 2:20 in the morning. A significant part of the crew was sleeping," he told reporters.
"There wasn't a lot of time in spaces that were open to the sea.
"So, it was traumatic. As to how much warning they had -- I don't know."
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 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.
It was not clear what caused the accident.
The collision 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.
There have reportedly been several collisions involving large vessels in the area over the past five years.
Japan's coastguard is conducting an investigation into the accident -- including interviewing the Japanese-owned container ship's Filipino crew -- although the US has primary jurisdiction in probing accidents involving military personnel.
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