"The families are being notified and being provided the support they need during this difficult time. The names of the sailors will be released after all notifications are made," the Navy said in a statement without specifying the number of bodies that had been recovered.
The bodies were taken to the US Naval Hospital in Yokosuka.
The 10,000-ton guided-missile destroyer and the ACX Crystal, a 29,000-ton container ship flagged in the Philippines, collided early Saturday local time, officials said.
The destroyer suffered severe damage to its starboard side, while the container ship sustained light damage.
Naval commanders praised the sailors for containing flooding caused by the collision, stabilizing the ship and sailing it back to port at the US naval base in Yokosuka.
While photos showed serious damage above the waterline, the container ship also did severe damage below it. Container ships like the Crystal have bulbous bows under the waterline and that portion of the cargo vessel plowed into the US warship.
The Fitzgerald had left the base Friday for routine operations.
Fitzgerald's commander, Cmdr. Bryce Benson, was evacuated by a Japanese naval helicopter while US military copters evacuated two injured US sailors. All three were in stable condition at the US Naval Hospital, said Cmdr. Ron Flanders, a spokesman for US Naval Forces Japan.
A US defense officials told CNN the Navy will soon announce the first of what is likely to be multiple investigations into the collision.
The initial Navy investigation will gather facts about what happened, with the 7th Fleet commander eventually deciding what disciplinary action is warranted, the official said.
Other investigations could come from the US Coast Guard and Japanese and Philippine authorities because of where the accident took place and the Philippine registry of the container ship.
The Fitzgerald is an Arleigh Burke-class guided-missile destroyer with a crew of approximately 330 sailors. The vessel is 505 feet long.
It completed $21 million in upgrades and repairs in February and is forward-deployed to Yokosuka, supporting security and stability in the Indo-Asia-Pacific region, the service said.
No one hurt on merchant ship
The ACX Crystal container ship is chartered by Japanese shipping company Nippon Yusen Kabushiki Kaisha (NYK) and owned by Dainichi-Invest Corporation, NYK said.
No one aboard the Crystal was hurt, and no oil spilled from the vessel, NYK said. It was back in port Sunday.
NYK and the ship's owner are cooperating with a Japan Coast Guard investigation into the collision, the shipping firm said.
"Our thoughts and deep concerns go out to all those directly affected," NYK said.
Photos of the Crystal showed damage to its bow.
The ship, which handles general cargo, is manned by a captain and a crew of 20, NYK said. It was built in 2008 and is about 730 feet long.