Head auditor George Munro listed several areas of concern at the council-owned harbours at Kinlochbervie and Lochinver.
These included an unauthorised bank account and the failure to record six fish landings worth£19,000 in two weeks.
Most surprising were reports of a large creditor list at a council-owned bonded warehouse in Lochinver, which sells spirits to foreign boats.
A staw poll of councillors present at the council's headquarters this week revealed no-one knew of the warehouse's existence. Roads and transport chairman Charlie King admitted the report did not look good.