"Serious deficiencies" in accounting systems at the Department of Arts, Heritage, Gaeltacht and the Islands were cited in the report.
It said preliminary audit tests disclosed that "the Department had been unable to reconcile its accounting records with those records maintained on its behalf by the Paymaster General - effectively the Department's banking records".
In addition, "discrepancies which had come to light" had not been resolved.
The report criticised the Department's omission of a receipt of £6 million from its accounts and noted "receipts collected by Waterways Ireland were incorrectly accounted for by the Department."