According to article 127 of the CPR, the Audit Authority ensures that audits are carried out on the management and control systems, on an appropriate sample of operations and on the annual accounts. It draws up an audit opinion on the annual accounts for the preceding accounting year and an annual control report setting out the findings of the audits carried out during the preceding accounting year.

The Audit Authority will prepare an audit strategy for the performance of audits. The audit strategy will set out the audit methodology, the sampling method for audits on operations and the planning of audits in relation to the current accounting year and the two subsequent accounting years. The audit strategy is updated annually from 2016 until and including 2024.

The Audit Authority is assisted by a Group of Auditors composed of a representative from each Member State participating in the programme in order to ensure uniform standards across the whole programme area. The representative of the Internal Audit and Investigations Department within the Office of the Prime Minister of Malta participates in the Group of Auditors and is responsible for providing the factual elements relating to expenditure on its territory that are required by the audit authority in order to perform its assessment.