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Taipei MRT Animated Images Planning of the Taipei Mass Rapid Transit (MRT) System began in 1975. Following the Executive Yuan's approval of the initial Taipei MRT network in April 1986, the Preparatory Office of DORTS was set up on June 27 that year. A reorganization of the Office brought about the Department's formal establishment on February 23, 1987, as a task-force unit under the jurisdiction of Taipei City Government.

Based on the organization rules, DORTS was a temporary government agency which was charged with the important responsibility of implementing Taipei MRT projects. At its inception DORTS consisted of five divisions, one center, and six offices with a total staff of 562. To meet the requirements of new tasks, such as joint development, quality assurance, and passenger transport services, DORTS was granted approval from the Executive Yuan on March 22, 1989, to add two new units – the Division 6 and the Quality Assurance (QA) Center, bringing the staff quota up to 740. Later, in conjunction with the establishment of the Taipei Rapid Transit Corporation Preparatory Office, DORTS transferred 188 employees from its Divisions 5 & 6 to the Taipei Rapid Transit Corporation (TRTC). The organizational structure of DORTS was reshuffled accordingly to reflect these changes.
On April 8, 1991, the Executive Yuan gave its approval for DORTS to make further organizational changes. At that time, DORTS headquarters consisted of 14 units with a staff of 604. Later, after the initial network was completed and commercial services began. As development of additional lines continued fewer lines were under simultaneous construction, and DORTS was then reorganized to adapt to MRT construction requirements. Taipei City Government reduced DORTS’ staff quota to 546 on April 24, 2003.
Then with the abolishment of Temporary Assigned Worker Assignment Act on June 19, 2015, Taipei City Government announced that the amendment to DORTS’ organization rules was completed on May 10, 2018 and went into effect on June 1, 2018. DORTS was changed into a permanent agency and reorganized to six divisions and five offices with the staff reduced to 459 employees. In addition, according to the original organization structure, five district project offices (East, North, South, Central, and Systemwide E&M) were established to carry out MRT construction. The Systemwide E&M Project Office has a staff quota of 133, while each of the other four project offices has a staff quota of 104 employees. In line with the reorganization, the four district project offices (except the Systemwide E&M) were merged into the First and Second District Project Offices. Each of the two project offices has a staff quota of 163 employees, while the Systemwide E&M Project Office retains a staff quota of 133 workers.