AVA- Among the injured is the USS Fitzgerald's commanding officer, who was taken to hospital by helicopter.
The destroyer collided with the container ship about 56 nautical miles (104km) south-west of Yokosuka.
Aerial images showed heavy damage to the Navy ship's starboard side after the collision at about 02:30 local time on Saturday (17:30 GMT Friday).
The ship's commanding officer, Cdr Bryce Benson, was 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 treatments for "lacerations and bruises", said the US 7th Fleet via Twitter.
By mid-afternoon local time, it said that all flooding on board the USS Fitzgerald was under control. It is not believed to be at risk of sinking.
The 7th Fleet also said the 154-metre (505ft) ship was now on its way to Yokosuka - under its own power, but with limited propulsion.