MG Rover filed for bankruptcy in April with debts of £1.4bn leading to the loss of more than 5,500 jobs.
The AIDB will examine audits of the 2003 accounts of Rover and parent Phoenix Venture Holdings.
Deloitte said it was disappointed by the news but would co-operate fully.
"We are confident that we will demonstrate that our work was carried out to the highest professional standards," Deloitte said in a statement.
An investigation into the collapse of MG Rover is also underway by the Department of Trade and Industry.
In May, trade secretary Alan Johnson appointed independent investigators to look into the group's accounts following an earlier probe by the Financial Reporting Council.
“The public interest requires that issues raised by the review panel and developments after 2003 when the last accounts were published be investigated by independent inspectors.
“I have asked them to report to me as quickly as possible and in a form which will enable the report to be made public,” said Johnson at the time.