Seven crew members are reportedly missing and one injured after a US Navy destroyer collided with a merchant ship off the coast of Japan, the country's coast guard reported.

Footage from the Japanese TV network NHK showed heavy damage to the mid-right side of the Navy ship and a person in a stretcher being lifted to a helicopter.

The US 7th Fleet said on its Facebook page that it is working with the Japanese Coast Guard to conduct a medical evacuation for a sailor. The fleet said the number of injuries is still being determined.

The Japanese Coast Guard said it received an emergency call from a Philippine- registered container ship ACX Crystal early on Saturday (local time) that it had collided with the USS Fitzgerald southwest of Yokusuka, Japan.

Coast Guard spokesman Yuichi Sugino said coast guard patrol ships and aircraft were headed to the scene but said that no further details were immediately available.

The Philippine ship is 29,060 tons and is 222.6 metres long, the coast guard said.

The Navy said that the USS Fitzgerald collided with a merchant ship 56 nautical miles southwest of Yokosuka, a city south of Tokyo that is home to a major US Naval base. A US defense official said there is flooding in three compartments of the Fitzgerald.

The 7th Fleet says the ship experienced flooding in some areas and it is heading back to Yokosuka. The fleet said the Fitzgerald has limited propulsion, and the ship suffered damage on the starboard side below the water line.

The fleet said the USS Dewey, medical assistance and two Navy tugs were being dispatched as quickly as possible and that Naval aircraft were being readied to help.

The Pacific Fleet said the extent of injuries and damage to the Fitzgerald are being determined, and the incident is under investigation.