Among the injured is the ship's commanding officer who has been taken to hospital by helicopter.
The Navy destroyer USS Fitzgerald collided with the container ship ACX Crystal about 103km south-west of Yokosuka at about 2.30am (local time) on Saturday.
The waterways approaching Tokyo Bay are busy with commercial vessels sailing to and from Japan's two biggest container ports in Tokyo and Yokohama.
Aerial images showed heavy damage on the destroyer's starboard side.
The ship's commanding officer, Commander Bryce Benson, is in a stable condition after being transferred to US Naval Hospital Yokosuka, according to Navy officials.
Two other sailors were flown to hospital by helicopter for treatment for "lacerations and bruises", the navy said.
It said earlier that the USS Fitzgerald had experienced flooding in some areas, and the full extent of injuries was being determined.
It also said the 154m ship was now on its way to Yokosuka - under its own power, but with limited propulsion.
The coast guard said the ACX Crystal container ship carried a Filipino flag and weighed just under 30,000 tonnes, about three times that of the USS Fitzgerald.
It sustained lighter damage to the port bow, according to Japanese national broadcaster NHK.
In a statement released on social media, US Navy operations chief Adm John Richardson said: "As more information is learnt we will be sure to share it with the Fitzgerald families and when appropriate the public. [...]
"All our thoughts and concerns are with the Fitzgerald crew and their families."
Photo: AFP Damage done to the USS Fitzgerald by the collision with the with Philippines merchant ship.