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The National Health Insurance Administration was previously known as the "Bureau of National Health Insurance" under the Executive Yuan and defined as a "financial and insurance public enterprise." When founded in 1995, the BNHI merged three existing health insurance programs – government employee insurance, labor insurance and farmers' health insurance – that covered only 50 percent of the population at the time and expanded into a comprehensive social insurance system that offered universal coverage based on the principles of sustainability and caring for the disadvantaged. The BNHI was repositioned in 2010 as an "administrative agency" and renamed as the NHIA in 2013 as part of a government reorganization plan and has ultimately emerged as a state-run national health insurance agency based on a single-payer model. Taiwan's NHI system is a social insurance program organized by the government under the jurisdiction of the Ministry of Health and Welfare. The ministry's NHI Committee helps plan and monitor NHI-related tasks, and its NHI Dispute Mediation Committee deals with NHI related disputes. The NHIA is responsible for managing health insurance affairs, medical quality, research and development, manpower training and information on the health care system. Its operations are funded out of the central government budget.

In addition to specialized groups and offices that plan and promote various health insurance measures, the NHIA has six regional divisions across Taiwan that handle insurance enrollments, premium collections, utilization review and reimbursements, and the management of contracted medical institutions. Twenty one liaison offices have been set up around the country to serve the public. As of June 30, 2015, the NHIA had 2,881 employees.