The grim announcement comes a day after Indonesia said the submarine was considered sunk, not merely missing, but did not explicitly say whether the crew was dead.
Officials had also said the KRI Nanggala 402′s oxygen supply would have run out early Saturday, three days after the vessel went missing off the resort island of Bali.
An underwater robot equipped with cameras found the lost submarine was lying in at least three pieces on the ocean floor at a depth of 838 meters (2,750 feet).
That's much deeper than the KRI Nanggala 402′s collapse depth of 200 meters (655 feet), at which point water pressure would be greater than the hull could withstand, according to earlier navy statements.
The cause of the disappearance was still uncertain.
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The navy had previously said an electrical failure could have left the submarine unable to execute emergency procedures to resurface.
An American reconnaissance plane, a P-8 Poseidon, landed early Saturday and had been set to join the search, along with 20 Indonesian ships, a sonar-equipped Australian warship and four Indonesian aircraft.
The German-built diesel-powered KRI Nanggala 402 had been in service in Indonesia since 1981 and was carrying 49 crew members and three gunners as well as its commander, the Indonesian Defense Ministry said.
Indonesia, the world's largest archipelago nation with more than 17,000 islands, has faced growing challenges to its maritime claims in recent years, including numerous incidents involving Chinese vessels near the Natuna islands.
