Intelligence and Enforcement Group. Under a Deputy Commissioner, this group gathers intelligence information related to Customs and economic activities; conducts internal inquiry and investigation; and exercises police authority.

Management Information System and Technology Group (MISTG). To ensure its continuing progress, the implementation of BOC's computerization program necessitated the creation of MISTG on January 9, 1998 under Executive Order No. 463. The need for the creation of a greatly expanded IT group was already reflected in the 1992 ISP as a support to the aim for BOC to assume direct management and control of IT facilities and services after the conclusion of the transitional facilities management arrangements under the PTCP contract. MISTG is headed by a Deputy Commissioner who is responsible for overall supervision of the different operating units.

Collection Districts. Each District is headed by a District Collector of Customs and collects duties, taxes and other charges accruing to the government; exercises police powers; supervises the entrance and clearance of vessels engaged in commerce; supervises and controls handling of foreign mail; and supervises all import and export cargoes and freight stations.