Singapore and Malaysia have dispatched ships to the area, and Australia, France and Germany have also offered assistance.
Pentagon spokesman John Kirby said: “Indonesia is a good friend and strategic partner.
“We were all deeply saddened to see the reports about their submarine and our thoughts and our prayers are with the Indonesian sailors, the Indonesian navy, and of course all their families.”
The German-built submarine joined the Indonesian fleet in 1981, the defence ministry said, and underwent a refit in South Korea that was completed in 2012.
The vessel was built in the 1970s and was said to be in good condition.