The U.S. Navy said on Friday that one of its destroyers collided with a Philippine-flagged merchant vessel southwest of Yokosuka, Japan, in the dead of night and Japanese media reported that seven U.S. crew members were missing.

The Navy said in a statement that the USS Fitzgerald collided with a merchant vessel at about 2:30 a.m. local time (1730 GMT), some 56 nautical miles southwest of Yokosuka, a rare incident on a busy waterway.

A U.S. official told Reuters that the Fitzgerald was still working to account for all personnel and could not confirm if any were missing.

The Navy said one injured U.S. sailor would be evacuated by a Japanese coast guard helicopter.

"The USS Fitzgerald suffered damage on her starboard side above and below the waterline," the Navy said in a statement.

It said the destroyer had experienced some flooding, and that the full extent of damage to the ship and injuries to its crew were still being determined. It said the Fitzgerald was operating under its own power, "although her propulsion is limited".

Kyodo news agency, citing the Japanese coast guard, said seven U.S. crew members were missing. Reuters could not immediately reach the Japanese coast guard to independently confirm the report.

A spokesman for the U.S. 7th Fleet said earlier that the ship was heading back to Yokosuka under its own power at 3 knots and would likely dock in a couple of hours.

Situated at the approach to Tokyo bay, Yokosuka and the waters to its south are busy with commercial vessels sailing to and from Japan’s two biggest container ports in Tokyo and Yokohama.

The USS Dewey and two Navy tugboats were being dispatched to provide assistance, the Navy said.

Japan's public broadcaster NHK showed aerial footage of the destroyer, which had a large dent in its right, or starboard, side. Images broadcast by NHK showed it had been struck next to its Aegis radar arrays behind its vertical launch tubes.

The images showed what appeared to be significant damage on the deck and to part of the radar. NHK also showed footage of the container vessel and said it was heading towards Tokyo under its own power.

Japan's Kyodo news agency reported that neither ship was in danger of sinking but that there was information that some crew may have gone overboard. It did not provide a source. Reuters could not immediately verify that account.

The 7th fleet said the collision was with the Philippine-flagged merchant vessel ACX Crystal. At around 29,000 tons displacement it is about three times the size of the U.S. warship.

A spokesman for the Philippines coast guard said he had heard of the accident but had no details since it was not in Philippine waters.

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.