For performing tasks under the Agency's scope of work, the following organisational units are established:
1. Director's Cabinet
2. Sector for management of horizontal processes
2.1. Service for Implementation of Technical Assistance and Audit of Financial Mechanisms
2.2. Service for Support to Audit Processes
2.3. Service for Finances and Accounting
3. Sector for Audit of Structural Instruments
3.1. Service for Audit of European Funds for Asylum, Migrations, Integration and Internal Security
3.2. Service for Audit of European Regional Development Fund and Cohesion Fund
3.2.1. Department for System Audit and Audit of Accounts
3.2.2. Department for Audit of Operations
3.2.3. Department for Legal Analysis
3.3. Service for Audit of Programmes under European Territorial Cooperation
3.3.1. Department for System Audit and Audit of Accounts
3.3.2. Department for Audit of Operations
3.4. Service for Audit of European Social Fund
3.4.1. Department for System Audit and Audit of Accounts
3.4.2. Department for Audit of Operations
4. Sector for Audit of Fisheries and Agricultural Funds
4.1. Service for Audit of European Agricultural Fund for Rural Development
4.1.1. Department for Audit of IACS measures
4.1.2. Department for Audit of Non-IACS measures
4.2. Service for Audit of European Agricultural Guarantees Fund
4.2.1. Department for Audit of IACS measures
4.2.2. Department for Audit of Non-IACS measures
4.3. Service for Audit of European Maritime and Fisheries Fund