"It is possible that during static diving, a blackout occurred so control was lost and emergency procedures cannot be carried out and the ship falls to a depth of 600-700 metres," the Indonesian Navy said in a statement.
The submarine was built to sustain pressure at a maximum depth of around 250 metres, an official said.
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Military analyst Soleman Ponto said it was too early to determine the fate of the submarine.
"We don't know yet whether the communication equipments were broken or the submarine has sunken. We have to wait for at least three days," he said.