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Japanese media said all seven of the sailors who had been reported missing were found dead.
A Seventh Fleet statement said the sailors were being transferred to a US naval hospital where they would be identified.
"The families are being notified and being provided the support they need during this difficult time," it said.
The Fitzgerald, an Aegis guided missile destroyer, collided with the Philippine-flagged merchant vessel more than three times its size some 56 nautical miles southwest of Yokosuka early on Saturday.
Three people were medically evacuated to the US Naval Hospital in Yokosuka after the collision, including the ship's commanding officer, Commander Bryce Benson, who was reported to be in stable condition, the Navy said.
The other two were being treated for lacerations and bruises and others injured were being assessed aboard the ship.
The USS Fitzgerald sailed into port on Saturday evening but search and rescue efforts by US and Japanese aircraft and surface vessels had been continuing for the seven missing sailors, the Navy said.
Benson took command of the Fitzgerald on May 13. He had previously commanded a minesweeper based in Sasebo in western Japan.
It was unclear how the collision happened. "Once an investigation is complete then any legal issues can be addressed," a spokesman for the US 7th Fleet said.
The U.S. Navy said the collision happened at about 2:30am local time, while the Japanese Coast Guard said it took place at 1:30am local time.
The Fitzgerald suffered damage on her starboard side above and below the waterline, causing "significant damage" and flooding to two berthing spaces and other areas of the ship, the Navy said.