Seven US Navy sailors remain missing in the Pacific Ocean more than 12 hours after their US destroyer collided with a container ship off the coast of Japan.

Key points: Missing sailors thought to be thrown into sea or trapped inside ship's damaged sections

Missing sailors thought to be thrown into sea or trapped inside ship's damaged sections Three injured sailors evacuated to hospital

Three injured sailors evacuated to hospital Unclear how collision happened, investigation underway

The US 7th Fleet said the USS Fitzgerald collided with the merchant ship 56 nautical miles south-west of the fleet's home base at Yokosuka, south of Tokyo, just before dawn on Saturday.

Rescuers were searching for the sailors who were thought to have been thrown into the sea or possibly trapped inside damaged sections of the destroyer, Japanese coast guard spokesman Yoshihito Nakamura said.

Family members were frantically trying to seek news, using social media to appeal for information from sailors aboard the ship as it slowly made its way to its home base.

The names of the missing sailors were being withheld pending notification of their families. US Navy personnel set up support and counselling services to help families as they sought updates on crew members.

"Just heard the sweetest voice and saw a wonderful face. He's okay. Thank you all for the prayers," Rita Schrimsher of Athens, Alabama, tweeted after speaking with her 23-year-old grandson, Jackson Schrimsher, via Facetime.

"It could have been worse, so we're grateful," she said by phone.

The Fitzgerald suffered damage on the right side below the water line and there was flooding in three compartments. ( AP: Eugene Hoshiko )

Footage from the Japanese TV network NHK showed Navy crew members working to pump water from flooded sections of the mid-right side of the USS Fitzgerald.

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The Navy said flooding was stabilised and sailors from the USS Dewey came aboard to assist in damage control.

Three crew members, including the ship's captain, Commander Bryce Benson, were evacuated by helicopter to a US naval hospital in Yokosuka. None of the crew of the container ship was reported injured.

Commander Benson was in stable condition, while the other two injured had lacerations and bruises, with other injuries being assessed, the Navy said.

Two other crew suffered cuts and bruises and were evacuated, it said. It was unclear how many others may have been hurt.

The Fitzgerald had limited propulsion after suffering damage on the right side below the water line and a US Defence official said there was flooding in three compartments.

The Navy, Japanese maritime defence vessels and the coast guard were working to stabilise the destroyer as it headed to shore, said Navy chief Admiral John Richardson.

"Right now we are focused on two things: the safety of the ship and the wellbeing of the sailors," said Admiral Scott Swift, Commander of the US Pacific Fleet.

The coast guard dispatched five patrol ships and an aircraft carrying medics to the site for search and rescue operations.

Investigation launched as limping US ship returns to port

The Fitzgerald, flanked by two tug boats and another support vessel, was brought back to its home port at the Yokosuka Naval Base.

A spokesman for the US 7th Fleet said the ship returned under its own power at three knots. A separate report said it was listing to its right as it slowly approached the port.

It was unclear how the night-time collision happened, and the US Navy said the incident was under investigation.

"Once an investigation is complete, then any legal issues can be addressed," a spokesman said.

Most of the more than 200 sailors aboard would have been asleep in their berths, some of which were reportedly flooded.

The ship, part of an eight-ship squadron based in Yokosuka, had in February completed $US21 million worth of upgrades and repairs.

Japan's Nippon Yusen KK, which charters the container ship, ASX Crystal, said in a statement it would "cooperate fully" with the Coast Guard's investigation of the incident.

At around 29,000 tons displacement, the container ship is about three times the size of the US warship, and was carrying 1,080 containers from the port of Nagoya to Tokyo.

The waterways approaching Tokyo Bay are busy with commercial vessels sailing to and from Japan's two biggest container ports in Tokyo and Yokohama.

ABC/wires