Jan Mason and Jim Miller are leading the audit and are set to report back by the end of the year.
Defence Minister Richard Marles said he was confident the two leads could meet the tight timeline.
"Now is the time to ensure the defence estate meets Australia's future security needs and allows effective, long-term management and sustainment, in line with the recommendations of the defence strategic review," he said.
The defence estate covers 2.8 million hectares across every state and territory and includes 70 major bases, over 72 training ranges and more than 30,000 built structures.
Upkeep is expected to cost at least $12.2 billion over the forward estimates.
The audit will aim to ensure Australia's bases are fit for purpose and meet national security needs.
Recommendations will include consolidating, cancelling and disposing of assets that are no longer needed and accelerating the planning and delivery of infrastructure.
Assistant Defence Minister Matt Thistlethwaite said this would include looking at more innovative investments.
"Maintaining such a large and diverse estate requires investment decisions based on where they will make the greatest contribution to defence capabilities," he said.
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