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The Internal Audit Service monitors the budgetary expenditure of the Ministry and its affiliated bodies, and the use of EU funds by the Ministry and its affiliated bodies. It supervises the functioning of internal controls to ensure the legality and effectiveness of the activities of the Ministry and its affiliated bodies.

The Service supervises the implementation of internal regulations and instructions on the activities of the Ministry and its affiliated bodies, the reliability of accounting information, and the accuracy and completeness of the records of the Ministry and its affiliated bodies.

The Service ensures not only the prevention of errors and fraud within the Ministry and its affiliated bodies but also the protection of assets and property of the Ministry and its affiliated bodies. Furthermore, the Service conducts procedures in the exercise of supervision by the supervisory institutions of Slovenia and the EU over the work of the Ministry and its affiliated bodies, prepares analyses and reports, and advises on making decisions to establish and improve the risk management systems, controls and management procedures in the activities of the Ministry and its affiliated bodies. It participates in project teams or other forms of cooperation.