The Indonesian Navy has found its missing submarine sunk well below survival depths and broken into at least three parts, as the country's president sent his condolences to relatives of the 53 crew.

"Based on evidence, it can be stated that the KRI Nanggala has sunk and all of its crew have died," Rappler News quoted on Monday military chief Marshal Hadi Tjahjanto as saying.

A remote-controlled underwater robot took photos of the ill-fated vessel lying on the ocean floor at a depth of 2,750 feet, Navy chief of staff Adm. Yudo Margono said.

More debris from the doomed Nanggala were also recovered, including an anchor and fluorescent orange safety suits for emergencies, Navy officials said.

The discovery comes a day after the Navy had first confirmed the retrieval of debris from the stricken vessel and declared it had sunk, effectively ending any chance of finding survivors.

The Indonesian vessel KRI Rigel also deployed an ocean-scanning ship to pinpoint the submarine's location using multi-beam sonar and a magnetometer, officials said.

Navy authorities and experts have not yet determined the cause of the submarine's sinking.

Indonesian officials previously said an electrical failure caused by a blackout could have rendered the submarine incapable of executing emergency procedures to resurface.

Margono said the crew were not to blame for the accident and that the submarine didn't experience a blackout, blaming "forces of nature."

"All of us Indonesians express our deep sorrow over this tragedy, especially to the families of the submarine crew," Indonesian President Joko Widodo said in remarks quoted by Reuters.