The Commissioner of Customs and Excise is the head of the department. He is assisted by the Deputy Commissioner. In July 2004, the department set up the Special Duties Branch to assist the Financial Services and the Treasury Bureau in conducting a study on the implementation of a Goods and Services Tax in Hong Kong. The department comprises six branches, each under a directorate officer. The six branches are:

• Administration and Excise Branch;
• Boundary and Ports Branch;
• Intelligence and Investigation Branch;
• Special Duties Branch;
• Trade Controls Branch; and
• Civil Secretariat.

2. The Administration and Excise Branch, headed by Assistant Commissioner (Administration and Excise), is responsible for all matters relating to dutiable commodities under the purview of the Financial Services and the Treasury Bureau, co-ordination of agency services under the purview of the four major policy bureaux, namely the Commerce, Industry and Technology Bureau, the Economic Development and Labour Bureau, the Financial Services and the Treasury Bureau, and the Security Bureau; taking care of international customs liaison and co-operation; and conducting study on the implementation of the Goods and Services Tax in Hong Kong. It is also responsible for the overall staff management and the general administration of the Customs and Excise Service, including planning and management of central resources and departmental facilities. The Branch comprises the Office of Dutiable Commodities Administration, the Office of Management Services, the Office of Service Administration, the Office of Training and Development, and the Customs Liaison Bureau.

3. The Boundary and Ports Branch, headed by Assistant Commissioner (Boundary and Ports), is responsible for all matters relating to customs control and facilitation functions at all entry and exit points under the purview of the Security Bureau. In particular, it is responsible for customs clearance and detection, prevention and interdiction of smuggling activities. The Branch comprises the Airport Command, the Control Points Command, and the Ports and Maritime Command.

4. The Intelligence and Investigation Branch, headed by Assistant Commissioner (Intelligence and Investigation), is responsible for all matters relating to narcotic drugs investigations under the purview of the Security Bureau, intellectual property rights protection under the purview of the Commerce, Industry and Technology Bureau, and protection of revenue levied on dutiable goods under the purview of the Financial Services and the Treasury Bureau. It is also responsible for the formulation of policies and strategies to further promote the use of intelligence and risk management in the department's operations, investigation and suppression of illicit trafficking in dangerous drugs, enforcement of the provisions of drugs/organized crime assets confiscation and control of chemicals. The Branch comprises the Customs Drug Investigation Bureau, the Intelligence Bureau, the Intellectual Property Investigation Bureau, the Revenue and General Investigation Bureau, and Special Task Force.

5. The Special Duties Branch, headed by Assistant Commissioner (Special Duties) and comprising two project teams, is responsible for a detailed study on the implementation of a Goods and Services Tax (GST) in Hong Kong and, in particular, on matters relating to collection of GST on imports. Since its establishment, the Branch has undertaken a series of studies on Customs control for consideration at the GST Study Committee led by the Permanent Secretary for Financial Services and the Treasury (Treasury). On 26 January 2005, the Special Duties Branch has been disbanded and integrated under the Administration and Excise Branch.

6. 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 purview of the Commerce, Industry and Technology Bureau and consumer protection matters under the purview of the Economic Development and Labour Bureau, as well as the overall staff management of the Trade Controls Officer Grade. The Branch comprises the General Investigation and Systems Bureau, the Trade Investigation Bureau, the Textiles Tactical Investigation Bureau (re-organized to CEPA and Transhipment Controls Bureau in 2005), the Trade Inspection and Verification Bureau, and the Consumer Protection and Prosecution Bureau.

7. The Civil Secretariat, headed by a Senior Principal Executive Officer as Customs Civil Secretary, is responsible for all matters concerning departmental administration, financial management, internal audit, and information technology development. The Civil Secretariat comprises the Office of Information Technology, the Office of Financial Administration, the Office of Departmental Administration, the Information Unit, and the Internal Audit Division.

8. Apart from the six branches, there are two teams and one group, namely the Formation Inspection Team, the Management Support Team, and the Complaints Investigation Group which are under the direct command of the Deputy Commissioner.

9. At the end of 2004, the department had an establishment of 4 947 posts. Of these, nine were directorate posts, 3 822 were posts of the Customs and Excise Service, 508 were those of the Trade Controls Officer Grade and 608 belonged to the General and Common Grades.