The Commissioner of Customs and Excise is the head of the Customs and Excise Department. He is assisted by the Deputy Commissioner. The department comprises five branches, each under a directorate officer. The five branches are:

• Administration and Development Branch;
• Boundary and Ports Branch;
• Excise and Operation Support Branch;
• Intelligence and Investigation Branch; and
• Trade Controls Branch

The Administration and Development Branch, headed by Assistant Commissioner (Administration and Development), is responsible for matters concerning overall staff management of the Customs and Excise Service, project planning and equipment procurement, provision of think tank and executive support services to the directorate, service quality and management audit, departmental administration, financial management, information technology development and internal audit; and the housekeeping of the Office of Service Administration, the Office of Planning and Development, the Office of Service Quality and Management Audit, the Office of Strategic Research, the Office of Departmental Administration, the Office of Financial Administration, the Office of Information Technology, the Internal Audit Division and the Information Unit.

The Boundary and Ports Branch, headed by Assistant Commissioner (Boundary and Ports), is responsible for matters relating to import and export controls under the purview of the Security Bureau and the housekeeping of the Airport Command, Control Points Command, and the Ports and Maritime Command.

The Excise and Operation Support Branch, headed by Assistant Commissioner (Excise and Operation Support), is responsible for matters relating to dutiable commodities under the purview of the Financial Services and the Treasury Bureau, the international customs liaison and cooperation and staff training; and the housekeeping of the Office of Dutiable Commodities Administration, the Customs Liaison Bureau, the Office of Management Services, the Office of Training and Development, the Special Duties Team and the Complaints Investigation Group.

The Intelligence and Investigation Branch, headed by Assistant Commissioner (Intelligence and Investigation), is responsible for matters relating to narcotic drugs and anti-smuggling activities under the schedule of the Security Bureau and issues relating to intellectual property under the purview of the Commerce, Industry and Technology Bureau; formulation of policies and strategies regarding the application of intelligence and risk management in Customs operations and the housekeeping of the Customs Drug Investigation Bureau, the Intellectual Property Investigation Bureau, the Intelligence Bureau, the Revenue and General Investigation Bureau and the Special Task Force.

The Trade Controls Branch, headed by a Senior Principal Trade Controls Officer as the Head of Trade Controls, is responsible for trade controls matters under the schedule of the Commerce, Industry and Technology Bureau and consumer protection matters under the schedule of the Economic Development and Labour Bureau.  The Trade Controls Branch comprises the CEPA and Transhipment Controls Bureau, the Trade Inspection and Verification Bureau, the Trade Investigation Bureau, the General Investigation and Systems Bureau and the Consumer Protection and Prosecution Bureau.