The Navy's 7th Fleet said on its Facebook page that the number of injuries was still being determined but a US official later confirmed seven were missing and two injured, including the ship's commander.
Seven US crew members were missing after a US Navy destroyer collided with a Philippine-flagged merchant vessel in southwest of Yokosuka, Japan, the Japanese Coast Guard reported on Saturday.
The US Navy said Cmdr. Bryce Benson, commander of the USS Fitzgerald, was among two sailors medically evacuated and in stable condition after being taken to a naval hospital.
TRT World's Nafisa Latic reports.
"The USS Fitzgerald suffered damage on her starboard side above and below the waterline," the Navy said in a statement.
It said the full extent of damage to the ship and injuries to its crew were still being determined. The Fitzgerald was operating under its own power, "although her propulsion is limited".
A spokesman for the US 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 US 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 US Navy's USS Lake Champlain collided with a South Korean fishing vessel but both ships were able to operate under their own power.