Three aboard the destroyer were treated at the U.S. Naval Hospital, including ship Commander Bryce Benson.
The collision had resulted in some flooding and damage to the ship's starboard side.
The U.S. Navy is searching for seven sailors after a destroyer collided with a merchant ship more than three times its size near Japan, according to the military.
"This has been a hard day", Vice Adm. Joseph P. Aucoin, the commander of the US 7th Fleet, said in a statement.
Seven Navy sailors were reported missing and the captain and at least two others were injured in the crash which happened just before dawn.
The guided-missile destroyer collided with a Philippine-flagged 730-foot container ship some 56 nautical miles southwest of Yokosuka, Japan around 2:30 am local. Authorities say the ship's flooding "has been stabilized", but seven sailors remain unaccounted for.
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Water was being pumped out of flooded areas and it was unclear how long it would take to get into the crushed mid-right side of the ship.
The U.S. 7th Fleet said on its Facebook page that the collision was with Philippine-flagged merchant vessel ACX Crystal.
Shortly after the collision the US made a request for support from the Japanese Coast Guard, which was the first on scene and continues to be the lead for search-and-rescue efforts, according to a release.
There was no immediate explanation as to the cause of the collision.
The ACX Crystal weighs 29,060 tonnes and is 730ft long, the coast guard said, much larger than the 8,315-ton Navy destroyer.
The Navy's 7th Fleet reported the developments in an update on the stricken ship that was nearing the port of Yokosuka in Japan.
U.S. Naval Forces Japan said an emergency family assistance center was established and families had phone numbers they could call for more information. Japan Coast Guard cutters IZUNAMI and KANO are on station, as well as a helicopter.
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The ACX Crystal - which sailed to a Tokyo port Saturday - is a commercial container ship with a Filipino crew, according to its Japanese owner, NYK Line.
A myriad of information is being analyzed on the cause of the collision, sources close to the matter have said, such as the exact locations of the two vessels, the speed they were traveling at, their routes, their radar and other surveillance capabilities, as well as the weather conditions at the time. The U.S. Navy Arleigh Burke-class guided missile destroyer USS Dewey served as an escort for the Fitzgerald and has also returned to Yokosuka.
Benson took command of the Fitzgerald on 13 May.
Aikawa said the USA ship is partially flooded because of damage and not capable of moving by itself.
Neither of the vessels involved in the collision were in danger of sinking, the Japan Coast Guard said earlier. A US naval vessel collided with a South Korean fishing ship in May.
Nippon Yusen K.K., the Japanese shipping company that operates the container ship that collided with a U.S. Navy destroyer, says its 20-member crew all safe. Now working with the Japanese Coast Guard to conduct a medevac via helicopter for one Sailor.
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