Names of the victims are being identified. Earlier, the US Navy said at least three sailors were injured and seven went missing after the collision.
The incident occurred 56 nautical miles southwest of Yokosuka city of Japan, causing damage in the right side and flooding in the destroyer.
The USS Fitzgerald camps in Yokosuka and mainly operates in the Pacific area and Japan Sea.
According to the US Navy, with capacity of about 29,000 tonnes, the Philippine-flagged ACX Crystal was three times bigger than the US destroyer. Meanwhile, the Japan's coastguard said none of the 20 members of the container ship were wounded.-