The submarine was taking part in a torpedo drill in North Bali waters but failed to relay results of the exercise as expected, said spokesman First Admiral, Julius Widjojono, Reuters reported.
The submarine, the KRI Nanggala 402, was built in Germany in 1981, has a cruising speed of 21.5 knots, and can take up to 34 passengers.
The navy spokesman and a spokesman for the defence ministry were not immediately available to respond to questions about how many crew were on board.