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Taipei City was upgraded to a national municipality in 1967. However, when it was placed directly under the leadership of the Taiwan Provincial Government, the Department of Health, Taipei City Government (hereafter, referred to as "the Department") and its subordinate medical care institutions primarily followed the organizational framework of the Taipei City Health Bureau. In light of the need to keep up with international trends in health and medical care developments, as well as the need to be in sync with the restructuring of our national health organization, and to realize our goals of making Taipei into a healthy city by global standards, action was taken in 2003 and 2004 to review and reform the Department's organizational structure and its subordinate medical care institutions. This was done with an aim to establishing unified responsibility-sharing mechanisms that clearly defined and helped manage each department's authority and responsibilities, so as to allow existing personnel to upgrade their overall service efficiency. The Department was reorganized from seven sections and eight offices to five divisions and seven offices. Ten medical care institutions were integrated into Taipei City Hospital, and the 12 district health stations were restructured into 12 district health centers. The restructuring plan was reviewed and approved by the 9th City Council at its 8th meeting of the 10th interim meeting on July 7, 2004 under Fu-Fa-3 Order No. 09312728300, effective as of January 1, 2005. The organizational structure and framework of the Department was released by the Taipei City Government in the Fu-Fa-Tsung Order No. 10632045700 on June 29, 2017, and shall be effective starting from July 1, 2017. The Department has reorganized into 9 divisions and 6 offices.
The ten municipal medical care institutions are: Renai, Zhongxiao, Heping, Zhongxing, Yanming, Women and Children, the Sanatorium, Chinese Medicine, Chronic Disease, and STD Control Institute. They have all been integrated into Taipei City Hospital to strengthen its planning, analysis, and assessment functions. Matters regarding quality control, medical education, community medicine, the procurement of supplies, human resources, and accounting are planned and managed as a whole to attain supervision and planning goals in accordance with the system's overall management strategies. These ten institutions also take part in the planning, analysis and assessment of local health policies, clarifying authority and delegating responsibilities for policy formation and implementation, and offer support to local health authorities.

The organization, missions and functions of the new health centers are different from those of the original health stations. The new health centers focus mainly on case management and health promotion to strengthen and promote public health functions, including the supervision of the establishment of community health promotion centers, the promotion of healthy workplaces, the management of volunteers, the promotion of breast-feeding, the prevention of accidents and injuries, the promotion of community mental health, and the provision of health education on specific issues. The disease control functions of the original health stations are now under the auspices of the Division of Disease Control and Prevention of the Department and the Disease Control and Prevention Branch (Kunming Branch) of Taipei City Hospital.