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The sailors were missing for more than 24 hours after the USS Fitzgerald collided with a much larger container ship before dawn yesterday, causing heavy damage and flooding areas of the destroyer.
"A number of sailors' bodies that were missing from the collision between USS Fitzgerald...And a merchant ship have been found," the US 7th Fleet said in a statement.
"As search and rescue crews gained access to the spaces that were damaged during the collision...The missing sailors were located in the flooded berthing compartments.
"They are currently being transferred to Naval Hospital Yokosuka where they will be identified," it added.
Japan's public broadcaster NHK updated an earlier report that claimed all seven missing sailors were found dead inside the ship, saying instead that "several" had been found.
The accident sparked a major US-Japanese search and rescue operation.
The 154-metre (500-foot) Fitzgerald was pulled by a tugboat back to its base in Yokosuka, south-west of Tokyo, on Saturday, where divers searched damaged areas of the guided missile destroyer.
The 222-metre Philippine-flagged ACX Crystal had large scrapes on its bow, but none of its 20 crew were injured, Japan's coastguard said.
The accident happened 56 nautical miles (104 kilometres) south-west of Yokosuka, in a busy shipping channel that is a gateway to major container ports in Tokyo and nearby Yokohama.
The missing sailors have not been identified.
"The families are being notified and being provided with the support they need during this difficult time," the Navy said.
"The names of the Sailors will be released after all notifications are made."
The cause of the accident is under investigation.