A South Australian Aboriginal lands group will have its finances checked for irregularities.
Federal Indigenous Affairs Minister Nigel Scullion said the forensic audit would examine government funds awarded to the Anangu Pitjantjatjara Yankunytjatjara executive board in 2014-15.
He said the government wanted to address longstanding issues with APY.
"We want to ensure all Commonwealth funding for services in the APY Lands is spent in accordance with funding agreements and the APY executive put in place a stable structure that is properly accountable - not just to government, but also to communities on the APY Lands," Mr Scullion said in a statement.
About 2500 people live on APY Lands in South Australia's far northwest but there has been a history of problems with governance, and the APY board has had seven general managers since 2010.
Last year, the SA government passed a law allowing the board to be suspended and an administrator appointed.
Problems further manifested in February with a series of violent incidents that led to 10 arrests.
SA Aboriginal Affairs Minister Kyam Maher said the state and federal governments were working together to ensure the board improved transparency and accountability.
"New funding will only be provided to the APY executive board if it can demonstrate an improvement in their governance and financial controls and systems," he said in a statement.
The audit follows the release of a grant review in May, which found a lack of financial controls and non-compliance.
The federal and state governments will each provide $50,000 for the audit, which will be done by Ernst and Young.
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