The audit was established by the Coalition to assess the scope of government spending and recommend reforms aimed at trimming the budget.
The government wants a surplus of at least $15 billion dollars within the next 10 years, but questions remain over how this will accumulate.
The government spends about $400 billion per year and nearly $12 billion of that is Indigenous expenditure.
Mr Abbott initially stated he wanted to be "the Prime Minister for Indigenous Affairs," but many believe his recent budget cuts suggest otherwise.
The effects of Abbott's budget cuts will not be clear until the end of February, when the first phase of the report is released.
A final copy is due at the end of March.
A directive from Finance Minister Mattias Corman was to consider the 1200 job cuts from the public-service sector promised during the election campaign.
There are more than 3000 Indigenous public servants and the previous government had plans to increase that number. But this is not guaranteed under Mr Abbott.