The Nigeria Customs Service is headed by the Comptroller-General and assisted by seven (7) Deputy Comptrollers-Generals heading the departments as follows:
- Finance Administration and Technical Service
- Tariff & Trade
- Enforcement, Investigation, and Inspection
- Strategic Research & Policy
- Human Resource Development
- Excise, FTZ, and Industrial Incentives
- Training and Doctrine Command (TRADOC)
These Deputy Comptroller-Generals have Assistant Comptroller-Generals heading each division under them while Comptrollers runs the affair of each unit under these divisions.
ACG (Headquarters) reports directly to the Comptroller-General along with the heads of some Special Units in addition to 4 Assistant-Comptroller-General (ACG) in the zones that coordinate the area commands under their respective jurisdictions.