- Disease Control Division: Vaccination, acute and chronic diseases control, infection control
- Food and Drug Division: License management, advertisement audit, offense management, consumer protection, industrial guidance, hygiene inspection
- Public Health Inspection Division: Inspection management, Eastern / Western / Southern / Northern / Central district inspection
- Medical Affairs Division: Medical affairs management, medical quality, emergency medical services
- Mental Health Division: Mental health, psychiatric care and prevention, suicide prevention, community mental health service
- Long-Term Care Division: Long-term care(LTC) management and services, special care
- Health Promotion Division: Health promotion, cancer prevention, women and infant healthcare, children and adolescent healthcare, adult healthcare, tobacco hazards control
- General Planning Division: Control and evaluation, integrated programs, international cooperation, R&D
- Administrative Service Office: Assets and document management, general affairs, and general accounting
- Laboratory Division: Public health inspection and food inspection
- System Administration: Public health information management
- Accounting Office: Final accounts and general accounting
- Statistics Office: Vital statistics and administration statistics
- Personnel Office: Personnel affairs, administration and management
- Government Ethics Office: Prevention, investigation and discipline of corruption; maintenance of administrative security