* Intense search under way for missing sailors
* Three sailors medically evacuated, including ship's commander
* Accident occurred in busy waterway south of Tokyo bay
* Cause has yet to be determined (Adds details, including search continuing after dark)
By Toru Hanai and Megumi Lim
TOKYO, June 17 (Reuters) - Search and rescue efforts went on after dark for seven U.S. sailors missing after the U.S. Navy destroyer USS Fitzgerald collided with a Philippine-flagged container ship more than three times its size off eastern Japan early on Saturday.
The Fitzgerald, an Aegis guided missile destroyer, collided with the merchant vessel some 56 nautical miles southwest of Yokosuka, the Navy said.
Three aboard the destroyer had been medically evacuated to the U.S. Naval Hospital in Yokosuka, including the ship's commanding officer, Cmdr. Bryce Benson, who was reported to be in stable condition, the Navy said. The other two were being treated for lacerations and bruises, while other injured were being assessed aboard the ship, it said.
The USS Fitzgerald sailed into port on Saturday evening but search and rescue efforts by U.S. and Japanese aircraft and surface vessels were continuing for the seven missing sailors, the Navy said. Their names are being withheld until the families have been notified, it added.
Benson took command of the Fitzgerald on May 13. He had previously commanded a minesweeper based in Sasebo in western Japan.
It was unclear how the collision happened. "Once an investigation is complete then any legal issues can be addressed," a spokesman for the U.S. 7th Fleet said.
The U.S. Navy said the collision happened at about 2:30 a.m. local time (1730 GMT), while the Japanese Coast Guard said it took place at 1:30 a.m. local time.
The Fitzgerald suffered damage on her starboard side above and below the waterline, causing "significant damage" and flooding to two berthing spaces and other areas of the ship, the Navy said.
The flooding was later stabilised, but it was uncertain how long it would take to gain access to those spaces once the ship docked, to continue the search for the missing, it said.
Back in Yokosuka, divers will inspect the damage and develop a plan for repairs, the Navy said.
The ship was able to operate under its own power with limited propulsion, the Navy said. The Japanese Coast Guard said separately the Fitzgerald was towed back to Yokosuka by a tugboat at about 3 knots.
Part of an eight-ship squadron based in Yokosuka, the Fitzgerald had in February completed $21 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 ship dwarfs the 8,315-ton U.S. warship, and was carrying 1,080 containers from the port of Nagoya to Tokyo.
None of the 20 crew members aboard the container ship, all Filipino, were injured, and the ship was not leaking oil, Nippon Yusen said. The ship arrived at Tokyo Bay around 5:00 p.m. (0800 GMT), sailing under its own power, the Coast Guard said.
The waterways approaching Tokyo Bay are busy with commercial vessels sailing to and from Japan’s two biggest container ports in Tokyo and Yokohama.
International maritime rules for collision avoidance do not define right of way for any one vessel, but provide common standards for signaling between ships, as well as regulations on posting lookouts.
Japan's public broadcaster NHK showed aerial footage of the Fitzgerald, which had a large dent on its right, or starboard, side. Images broadcast by NHK showed it had been struck next to its Aegis radar arrays behind the vertical launch tubes.
Such incidents are rare.
In May, the U.S. Navy's USS Lake Champlain collided with a South Korean fishing vessel but both ships were able to operate under their own power.
The 7th Fleet commander, Vice Admiral Joseph Aucoin, thanked the Japanese Coast guard in a post on the fleet's Facebook page, adding: "We are committed to ensuring the safe return of the ship to port in Yokosuka." (Additional reporting by Idrees Ali, Phil Stewart in Washington; Tim Kelly, Linda Sieg, Kiyoshi Takenaka, Chang-Ran Kim and Elaine Lies in Tokyo, Raju Gopalakrishnan in Manila, Chizu Nomiyama in New York; Writing by Yara Bayoumy and Chang-Ran Kim; Editing by Bill Tarrant and Adrian Croft)