The SMESA is headed by one Director General, two Deputy Director Generals and one Chief Secretary. The organization of the SMESA is divided into 4 divisions (Planning Division, Management Consulting Division, Startup and Incubation Division, Financial Development Division) and 4 offices (Secretariat, Personnel Office, Civil Service Ethics Office, Accounting and Statistics Office.) The Central Taiwan Service Office and Southern Taiwan Service Office also provide service to SMEs.

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