Missing debris has been found around the last dive area, and it's believed the sub resides thousands of feet below the surface, well beyond its survivable limit.
Military chief Hadi Tjahjanto said an oil slick and parts of the submarine were found near its last dive off Bali confirms the vessel had sunk.
AP quoted Navy Chief Yudo Margono as saying, "If it's an explosion, it will be in pieces. The cracks happened gradually in some parts when it went down from 300 meters to 400 meters to 500 meters ... If there was an explosion, it would be heard by the sonar."
The KRI Nanggala 402 sub was built in Germany in 1981 and updated in 2012. It's believed the vessel sits at a depth of 2,300 feet, well beyond the water pressure the hull can withstand.
Margono said search teams found a torpedo straightener, prayer rugs, coolant pipe, and a grease bottle for the periscope.
"With the authentic evidence we found believed to be from the submarine, we have now moved from the 'sub miss' phase to 'sub sunk,'" Margono concluded.
And unfortunately for the crew, the sub was never retrofitted with a rescue system.
The sunk sub has suffered the same fate as a missing Argentine submarine that disappeared a few years back. Its wreckage wasn't located until a year later, long after its crew had been condemned to a watery fate after the vessel "imploded".