The ship's captain, Commander Bryce Benson, was airlifted to the US Naval Hospital in Yokosuka and was in a stable condition with a head injury, the US navy's 7th Fleet said in a statement.
USA 7th Fleet Vice Admiral Joseph P. Aucoin said the search was continuing in a statement released almost 24 hours after the USS Fitzgerald, an Aegis guided missile destroyer, collided with the much larger Philippine-flagged merchant vessel 56 nautical miles southwest of Yokosuka.
Footage from the Japanese TV network NHK showed navy crew members working to pump water from flooded sections of the crushed mid-right side of the USS Fitzgerald.
Japanese news agency NHK reported, citing the coast guard, that in addition to seven missing USA sailors, one was injured in the crash.
"As more information is learned, we will be sure to share to it with the Fitzgerald families and when appropriate the public", read a statement from Adm. John Richardson.
USA and Japanese ships continued searching well after dark for the missing sailors.
The Japan Coast Guard has confirmed that seven crew members of a U.S. Navy destroyer are missing after a collision with a Philippine-flagged merchant ship off the coast of Japan.
The merchant vessel involved in the collision is the ACX Crystal based in the Philippines.
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.
Because the collision happened at night, most of the ship's crew were asleep in their berths.
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The navy said that the collision occurred 56 nautical miles south-west of Yokosuka, home to the 7th Fleet.
The coast guard is investigating the accident with the U.S. Navy and questioned the crew members of the 29,060-ton ACX Crystal, operated by Japanese shipping firm Nippon Yusen K.K., with an eye on possible endangerment of traffic caused by professional negligence.
Admiral Scott Swift, commander of the US Pacific Fleet, said: "Right now we are focused on two things: the safety of the ship and the well-being of the sailors".
U.S. Naval Forces Japan said an emergency family assistance center was established and families had phone numbers they could call for more information.
The Japanese coast guard led the search teams. The port side of the Filipino vessel was damaged, the coast guard said. Two Japanese coast guard cutters with helicopters were helping.
The container ship is docked in Tokyo Bay.
NHK footage on Saturday morning showed a person in a stretcher being taken up to a helicopter from the deck of the USS Fitzgerald. "Thank you to our Japanese allies for their assistance", President Donald Trump tweeted after the ship returned to base in Japan with the help of two tug boats after 6 pm local time. It is unclear how fast the destroyer was traveling when it and the merchant ship collided.
"We can't comment on the accident as it's being handled by the Japanese coast guard", a company spokesman told AFP.
The Pacific Fleet said the extent of injuries and damage to the Fitzgerald are "being determined", and the incident is under investigation.