Both warships were diverted from separate deployments to the search zone off the coast of Bali.
The Defence Department said HMAS Ballarat was equipped with sonar capabilities and a MH-60R helicopter. It was expected to arrive at the search area yesterday.
HMAS Sirius is currently off the coast of Brunei and is expected to reach the search area early next week.
Fleet commander Rear Admiral Mark Hammond said the two Australian ships would help expand the search area.
“My thoughts are with the submariners of KRI Nanggala, their families and the Indonesian people,” Rear Admiral Hammond said.
“As always, we stand ready to assist our fellow mariners in the Indonesian Navy.”
The Indonesian submarine went missing on Wednesday with 53 sailors on board.
“We lost contact (with the vessel) yesterday at 3am, so it can last until Saturday 3am,” naval chief of staff Yudo Margono said.
The US and Singapore militaries are also joining the search operation.
Australian Strategic Policy Institute senior analyst Marcus Hellyer said earlier this week that things were looking “very grim” for the submarine crew.
“There’s lots of things that can go wrong on submarines,” Dr Hellyer told nine.com.au.
“If a submarine has an accident at sea, it tends to be catastrophically bad.”
An oil slick has been spotted in the spot where the submarine dived from the surface, but aside from that, there is no trace of the KRI Nanggala-402.
And most submarines, including the KRI Nanggala-402, are not designed to survive more than a few hundred metres underwater.