The Bureau of Customs is headed by the Customs Commissioner. He is assisted by six (6) Deputy Commissioners, one (1) Assistant Commissioner and seventeen (17) District Collectors who supervise the country's principal ports of entry.
Internal Administration Group (IAG). Under a Deputy Commissioner, this group assists the Commissioner in the formulation of policies and in the setting up of objectives relative to financial, administrative, personnel, planning and management improvement services of the BOC; represents the Commissioner in meetings and conferences; signs memorandum circulars; and reviews official communications and documents relevant to internal administration.
Revenue Collection Monitoring Group (RCMG). Under a Deputy Commissioner, this group maintains an accounting of revenues collected; administers the legal requirements of the BOC; provides information and analysis of collection statistics; and audits liquidated entries and bonds.
Assessment and Operations Coordination Group (AOCG). Under a Deputy Commissioner, this group gathers and publishes values of commodities imported into the country; and monitors implementation of rules and regulations governing assessment, end processing of goods for exports, warehousing and support operations, and auction and disposal activities.
Intelligence Group (IG). Under a Deputy Commissioner, this group gathers intelligence information related to Customs and economic activities; conducts internal inquiry and investigation; and develop effective countermeasures to combat corruption, smuggling, and other forms of customs fraud.
Enforcement Group (EG). Under a Deputy Commissioner, this group exercises police authority to
secure the country's ports and BOC installations; and to protect cargoes and properties inside the customs zone.
Management Information System and Technology Group (MISTG). 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.
Post Clearance Audit Group (PCAG).Customs Memorandum Order (CMO) No. 32-2017 reactivates the Post Clearance Audit Group (PCAG) formerly known as Post Entry Audit Group (PEAG). PEAG was created in 2003 under EO 160-2003 and tasked to perform post-clearance audit work of the Bureau of Customs. In 2013, the functions of PEAG was transferred to the Department of Finance until President Rodrigo Duterte signed EO No. 46 on October 2017 returning the post-clearance audit function to the BOC. PCAG is headed by an Assistant Commissioner who has direct supervision and control over the management of the operating units of PCAG, which include the Trade Information and Risk Analysis Office and Compliance Assessment Office.
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.