The discovery came when divers were sent down to search inside the USS John S McCain, now berthed at Singapore's Changi naval base.
The collision with a Liberian-flagged ship happened before dawn on Monday as the US vessel made a routine port call.
The US has since ordered a worldwide "operational pause" of its navy fleet.
It was the fourth crash involving a US Navy ship in a year, and the second in the past two months.
The collision ripped open the port side of the US vessel, flooding parts of the ship including crew compartments.