The Comptroller-General of Customs is Col. Hameed Ibrahim Ali (Rtd). He is responsible for the overall management and direction of the Service. He is equally the accounting officer of the service and the Vice Chairman of the Nigeria Customs Service Board, which is chaired by the Honourable Minister of Finance.

By virtue of delegated authority, the Comptroller-General is authorized to issue guidelines and prescribe internal instructions to Customs personnel in accordance with the governments rules and regulations as they affect the statutory functions of the Customs Service.

In the discharge of his duties, the Comptroller-General is assisted by six Deputy Comptrollers-General each heading a department.