The Fitzgerald was struck by the Philippine-registered container ship ACX Crystal. Bryce Benson, is among the injured according to a statement by the U.S. Navy.
Japan's public broadcaster NHK showed aerial footage of the destroyer, which had a large dent in its right, or starboard, side.
The warship was towed back to Yokosuka, escorted by a Japanese coast guard ship, naval officials said.
Nippon Yusen K.K., the Japanese company operating the merchant vessel, said the 20 member Filipino crew aboard the ship was safe.
The accident 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.
The Fitzgerald, an Aegis guided missile destroyer, sailed back to its home port in Japan early Saturday evening, while USA and Japanese rescue teams were continuing their search for the missing crew members - who have not been named - more than 12 hours after the destroyer's collision with the ACX Crystal, a Philippine-registered container ship. The Philippine-flagged container ship was berthed at Tokyo's Oi wharf, where officials began questioning crew members about the cause of the crash.
The USS Fitzgerald requested the assistance of the Japanese coast guard after the collision occurred at approximately 2.30 a.m. Saturday.
Family members were frantically seeking news, appealing via social media for calls from sailors aboard the ship. "Thank you to our Japanese allies for their assistance".
The container ship is docked in Tokyo Bay.
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Sailors also could have been trapped in compartments below deck, Schuster said, pointing out that container ships have a bulbous bow below the water line, which may have plowed into the USA warship. Rita Schrimsher, of Athens, Alabama, told the Associated Press that she was relieved after speaking with her 23-year-old grandson Jackson Schrimsher.
"Our thoughts and prayers are with the families and colleagues of the injured and missing USA personnel", it said.
The Pentagon set up a hotline for families of the crew of the Fitzgerald to check on the status of loved ones.
The Japanese coastguard said the Fitzgerald was experiencing some flooding but was not in danger of sinking, while the merchant vessel was able to sail under its own power.
Another two US sailors were medically evacuated and taken to a hospital in Yokosuka for treatment for "lacerations and bruises", according to the USA naval fleet in Japan. United States navy aircraft would also join Japan's coast guard and maritime self-defence force helicopters, ships and aircraft "to render whatever assistance may be required".
The Fitzgerald is the second command for Benson, a 1999 Naval ROTC graduate of Marquette University.
A U.S. Navy official said after the collision that the bridge was damaged and communication with the ship was limited and hard.
The Pacific Fleet said the extent of injuries and damage to the Fitzgerald are being determined, and the incident is under investigation.
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