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The Joint Internal Audit Service provides advice in the preparation of organisational regulations with regard to the operation of control points, supervises the operation of budget users and their organisational units, and evaluates and assesses the performance of tasks.

It monitors the reports of budget users and organisational units and of external supervisory authorities (the Budget Supervision Office at the Ministry of Finance and the Court of Audit of the Republic of Slovenia) and prepares bases for decision-making concerning administration management and quality improvement in the utilisation of funds within the framework of adopted policies and development strategies.

In addition to regular audits (in accordance with annual plans based on the strategic five-year plan), it also conducts extraordinary audits.