They were to take part in a live-fire exercise near Banongan beach of East Java's Situbondo district with tanks, artillery, infantry and attack helicopters, a joint landing operation and a non-combat evacuation used for a disaster.
The four-day Keris Woomera 2024 exercise highlighted the co-operation between the countries strengthened by the recent signing of the Australia-Indonesia Defence Co-operation Agreement.
Although Indonesia is often presented as one of Australia's most important neighbours and strategic allies, the relationship has fluctuated.
Recent disagreements include allegations that Australia had wiretapped private phone calls of a past Indonesian president, Indonesia's use of capital punishment on Australian drug smugglers, and the smuggling of migrants.
The exercise is part of Indo-Pacific Endeavour 2024, taking place in Australia and Indonesia. (AP PHOTO)
"This joint exercise aimed to strengthening the partnership between Indonesia and Australia as we are building trust and to increase capabilities and interoperability," said Lieutenant Colonel Empri Airudin, who lead the Indonesian delegation.
"It can also be regarded as a way of maintaining security and stability in the region."
The exercise was also part of Indo-Pacific Endeavour 2024, Australia's largest international engagement activity in the region, taking place in Australia and Indonesia, Commander of the Australian Amphibious Task Force Captain Chris Doherty told reporters on Wednesday.
"This bilateral exercise will test all facets of the Australian Amphibious Task Force, and allow all its components to work effectively together as a cohesive team with our Indonesian partners," he said, adding the KW24 could provide the troops of the two nations with the ability to rapidly deploy forces in response to a range of missions.
Analysts consider Indonesia's defence a priority of new President Prabowo Subianto.
He wants to expand his military by buying submarines, frigates and fighter jets and wants to initiate more defence co-operation with various countries.
Indonesia has held military exercises with other countries, including the Russian navy on November 4 in Indonesia's East Java seas, as Russia's invasion of Ukraine brought renewed concerns over China's assertiveness in the Indo-Pacific.
In October, Indonesia said its patrol ships drove away a Chinese coast guard ship that disrupted a survey being undertaken by a state-owned energy company in a part of the South China Sea disputed by both countries.
China has rapidly expanded its military and has become increasingly assertive in pursuing territorial claims in the South China Sea, which Beijing claims virtually in its entirety.
The tensions have led to more frequent confrontations, primarily with the Philippines and Vietnam, though the longtime territorial disputes also involve Malaysia, Indonesia, Brunei and Taiwan.
However, during Subianto's first overseas visit as Indonesia's new leader to Beijing during weekend, he called for collaboration rather than confrontation with China after the signing of $US10 billion in new deals at a business forum before departing to the US on Sunday.
He and Chinese President Xi Jinping agreed to hold a first-ever joint meeting of their foreign and defence ministers in 2025.