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- Director：Manage overall matters in the airport, direct and supervise subordinates.
- Deputy Director：Assist Director to manage the airport affairs.
- Business Services Section：In charge of airport business operation, equipment maintenance, and passenger services.
- Engineering Section：In charge of the management and maintenance of airport facilities.
- Filght Operations Section：In charge of inspection of the air safety, attendants, aircrafts, fire rescue, etc.
- Planning and General Affairs Section：In charge of the annual plan, research & development, assassment, rules and regulations, documentations, properties, payments, and other affairs that don't belong to other offices.
- Accounting Office：In charge of accounting and statistics etc.
- Personnel Office：In charge of manpower and personnel management.
- Operational Security Section：In charge of information system, terminal cleaning, and low power electrical facilities.
- Civil Services Ethics office：In charge of personnal ethic assessment, and government ethics supervision.
- Hengchun Airport：In charge of flight safety, operation, security and emergency processing in Hengchun Airport.