Adm. Scott Swift, commander of the U.S. Pacific Fleet, said Tuesday the remains were located in sealed compartments of the warship. The Malaysian Navy, which is supporting the search, said they have identified "potential remains."
The USS John S. McCain sustained damage on its port side aft, or left rear, from the collision with the Alnic MC on Sunday, the Navy's 7th Fleet said.
Five people were injured as a result of the collision.
The Navy said Osprey aircraft and Seahawk helicopters from the USS America were working to search for the missing sailors. It also said tugboats and Singaporean naval and coast guard vessels were in the area to render assistance.
The Strait of Malacca is a narrow body of water between Malaysia to the northeast and Indonesia to the southwest, with the city-state of Singapore at the tip of the Malay Peninsula.
The collision is the second involving a ship from the Navy's 7th Fleet in the Pacific in two months. Seven sailors died in June when the USS Fitzgerald and a container ship collided in waters off Japan.
The Fitzgerald's captain was relieved of command and other sailors were being punished after the Navy found poor seamanship and flaws in keeping watch contributed to the collision, the Navy announced last week. An investigation into how and why the Fitzgerald collided with the other ship was not finished, but enough details were known to take those actions, the Navy said.
The Japan-based 7th Fleet said the McCain had been heading to Singapore for a routine port visit when the collision occurred.
The ship is based at the 7th Fleet's homeport of Yokosuka, Japan. It was commissioned in 1994 and has a crew of 23 officers, 24 chief petty officers and 291 enlisted sailors, according to the Navy's website.
The warship is 505 feet in length.
The Alnic MC is a 600-foot oil and chemical tanker.
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