"We have evaluated it from the beginning and we believe this is not a human error, but more due to natural factors," he said in Bali on Sunday, April 26, without elaborating on what those factors were.
Margono said he believed that there was no human negligence and that the submarine had "followed all procedures needed".
The navy previously said an electrical failure could have left the submarine unable to execute emergency procedures to resurface.
But Admiral Margono said on Sunday he wasn't sure about a possible black-out as the cause, because he said during the diving process all the lights were still on.
"This means that the power was not immediately lost when diving," he said.
However, he said to determine the exact cause, they will investigate the remaining parts of the submarine.
The German-built submarine was more than 40 years old — it was constructed in 1978 — and it has been nine years since its last refit.
Military officials said the submarine went for maintenance in South Korea in 2009 and 2012, and its dive depth increased to around 250 meters.
They said the upper structure of the ship was partially replaced, while the weapons, sonar, radar, combat control, and propulsion systems were upgraded.
Owen said all we know for now is that the submarine sunk and that we won't know more until detailed analysis and research can be done.
"All the evidence that's coming up is just reinforcing that it was probably … a quick end to the submarine," he said.