They arrived with barely an acknowledgment from the Indonesian military, but that HMAS Adelaide and HMAS Toowoomba were docked for two days at a Jakarta port speaks volumes.

Their presence in Indonesian waters is a sign of stability in relations after a military spat earlier this year, and so that they were allowed to dock at all was seen as a welcome in itself.

HMAS Adelaide, Australia's most sophisticated helicopter landing ship, is leading the most significant Australian military mission in Asia in more than three decades as part of the Indo-Pacific Endeavour, an exercise that has annoyed China.

The Australian ships were not completely ignored during the two day stay in Jakarta and they did receive a brass band farewell from the Tanjung Priok port on Tuesday morning.

Australia and Indonesia saw a blip in military ties in January when some cooperation was suspended over what Indonesia deemed offensive material about West Papua at a special forces base in Perth.

Since then the suspension has been lifted and both nations have stressed the need for freedom of navigation in the contested South China Sea.

The HMAS Adelaide, a Canberra class assault ship, weighs 27,800 tonnes and measures 230 metres in length.

HMAS Adelaide is leading a fleet of six Navy ships visiting Asian neighbours. ( Supplied: Royal Australian Navy )

The ship is designed to provide medical and humanitarian assistance during regional emergencies with a 40-bed hospital and two operating theatres on board.

Its 200-metre flight deck can carry up to 12 helicopters and more than 100 vehicles can be stored on board.

It is leading a fleet of six Navy ships currently visiting Asian neighbours, including Malaysia, the Philippines and significantly the Korean Peninsula.

China has accused Australia of using the exercise to please the United States and expects the ships to pass through the South China Sea.

HMAS Adelaide and HMAS Toowoomba are now on the way to Malaysia.