- Director General of the National Customs Agency
- Secretary General
- Inspectorate
- Security Unit
- Internal Audit Unit
- Financial and Economic activities and Property Management Directorate
- Legal Directorate
- Human Resource Department
- Administrative Service Directorate
- National Тraining Centre Directorate
- Customs Regimes and Procedures Directorate
- Excise Duties Directorate
- Tariff Policy Directorate
- Post - Clearance Control Directorate
- Customs Intelligence and Investigations Directorate
- Customs Statistics and Automation Directorate
- International Relations Directorate
- Central Customs Laboratory Directorate

