Navy chief Admiral John Richardson said US Navy, Japanese maritime defence vessels and the Japanese coastguard were working to stabilise the badly-damaged ship.
The Japanese Coast Guard said it received an emergency call from a Philippine-registered container ship ACX Crystal at around 2:20 a.m. (1720 GMT Friday) that it had collided with the USS Fitzgerald at a location about 12 miles southeast of the Irozaki cape. Benson was one of four injured sailors who needed to be flown to a naval hospital in Yokosuka, Japan, reports the CNN. "The collision resulted in some flooding", the Navy said.
The Fitzgerald is an Arleigh Burke-class guided-missile destroyer with a crew of approximately 330 sailors.
The Japanese Coast Guard is on scene and providing assistance at the request of the U.S. Navy.
Coast guard official Takeshi Aikawa said seven crew members are unaccounted for, and one had a head injury.
The area is particularly busy with sea traffic, said Yutaka Saito of the coast guard. "Once an investigation is complete then any legal issues can be addressed", the 7th Fleet spokesman said.More news: Two arrested at anti-Sharia Law protest
The Japanese Coast Guard said the destroyer was experiencing some flooding but was not in danger of sinking, while the merchant vessel was able to sail under its own power.
The Navy says the USS Dewey, medical assistance and two Navy tugs are being dispatched as quickly as possible.
Japan's public broadcaster NHK showed aerial footage of the destroyer, which had a large dent in its right, or starboard, side.
"The extent of number of personnel injuries is being determined", the 7th Fleet said in a statement earlier.
Schuster said the larger size of the container ship compared to the U.S. destroyer left the smaller ship vulnerable in the collision.
No damage below the waterline was apparent from the images although damage on the deck and to part of the radar appeared significant.