The country's navy had said earlier that it considered the crew of 53 dead, an assessment that has now been confirmed with photos of the ship's wreckage.
The sub went missing early Wednesday morning off the coast of Bali during a training exercise, and Indonesian military officials estimated the sailors would run out of oxygen early Saturday.
The Pentagon says it will send airborne assets to help with the search as Indonesian officials say oxygen for the submarine - if still intact - may by now be exhausted.
Rescuers are scouring the Bali Sea for a submarine that disappeared this week. Officials say if the crew is still alive, they're expected to run out of oxygen by Saturday.
Category 2 Cyclone Seroja raked the area as the storm tracked on a course for Western Australia, dumping heavy rain on the islands and triggering mudslides that buried homes and people.
The memory unit from the cockpit voice recorder belonging to the Sriwijaya Air Boeing 737-500 that crashed into the Java Sea has been recovered, investigators say. All 62 people aboard were killed.
Two suicide bombers attacked a Roman Catholic church compound in Makassar on Sunday. Indonesian President Joko Widodo condemned the attack as an "act of terrorism."
Investigators say an engine throttle appears to have malfunctioned while the autopilot was engaged, possibly contributing to last month's crash of a Boeing 737-500 that killed all 62 people aboard.
Indonesia, an archipelago of 270 million people, sits along the Pacific "Ring of Fire," which leaves the country prone to earthquakes, tsunamis and eruptions.