The FDA is headed by the Director-General (DG), who is appointed by the President of the Philippines.

The Office of the Director General is assisted by two Deputy Director Generals (DDG), the DDG for Administration and Finance Office and the DDG for Field Regulatory Operations Office.

The FDA has four Centers, that are headed by the Center Directors. The Centers are named according to the major health product categories they regulate, as follows:

  • The Center for Drug Regulation and Research
  • The Center for Food Regulation and Research
  • The Cosmetics Regulation and Research
  • The Center for Device Regulation, Radiation Health and Research

The following Offices, headed by Directors, support the operations of the four Centers, as follows:

  • The Policy, and Planning Office and,
  • The Legal Services Support Center, which are both under the Office of the FDA Director General,
  • The Administration and Finance Office, which is under the Office of the Director General for Administration and Finance; and
  • The Regional Field Offices, including the National Capital Region-Regional Field Office, which are under the Office of the Deputy Director General for Field Regulatory Operations Office 

As provided by law, the FDA maintains a Central Laboratory on top of the Laboratory Support Division of each Center.

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