The development of the environmental protection system in Taiwan can be divided into the following five stages:

Stage 1: History Before March 17, 1971

• The Taiwan Provincial Government was founded in 1947 and the Department of Health was expanded to include public hazard prevention and control, as well as improvement and promotion of environmental sanitation. The Experimental Institute of Environmental Health of Taiwan Province was set up by the Department of Health in 1955 to take charge of surveys, studies, management of water sanitation, waste water treatment, garbage disposal, water quality control, general environmental health, air pollution control, radiation safety, and noise control.
• The Taipei City Government integrated the Municipal Cleaning Unit and Sewage Treatment Commission into the Department of Environmental Cleaning in October 1968, to take charge of air and water pollution control and waste treatment. The Department of Health under the Taipei City Government was given the responsibility of public hazard control.
• Section II of the Public Health Bureau in every city and county of Taiwan was designated as the responsible agency for promotion and protection of environmental health.
• The Department of Health was established under the auspices of the Ministry of the Interior to be in charge of infectious disease prevention, epidemic control and surveillance, international health inspection and quarantine, environmental sanitation, public health facilities, and management of medicine. The Ministry of Economic Affairs set up the Industrial Development Bureau in 1969. Section 7 of the IDB was responsible for the management of industrial waste gas and water emissions as well as the prevention and mediation of public hazards.

Stage 2: From March 17, 1971 to January 28, 1982

• In March 1971, the Department of Health, Executive Yuan, set up the Environmental Health Division which was led by Directors Shu Cheng-bei and Chuang Chin-yuan, successively. This Division was in charge of: the management and monitoring of garbage and sewage disposal in public health facilities, public spaces, and food processing plants; the use of pesticides; studies, guidance, and supervision of air, water and noise pollution control. In addition, the Ministry of Economic Affairs also set up the Water Pollution Control Section under the Water Resource Integrated Planning Commission, to take care of water pollution control.
• In addition to the Department of Health and the Experimental Institute of Environmental Health, the Taiwan Provincial Government set up the Water Pollution Control Institute under the Construction Department to take charge of pollution control, watershed designation, water pollution control planning and training, permit issuing, dispute resolution and execution, as well as supervision, auditing, and research on control technology for waste water treatment facilities.
• The Kaohsiung City Government integrated the Cleaning Unit and Sewage Treatment Commission into the Department of Cleaning Management, to take charge of garbage disposal and drainage cleaning. In July 1979, as Kaohsiung City was upgraded to a municipal level city, the Department was expanded to become the Department of Environmental Administration to manage matters related to environmental cleaning and control of public hazards.

Stage 3: From January 29, 1982 to August 21, 1987

• The Executive Yuan passed the "Environmental Protection Act in the Taiwan Area" in April 1979 to comprehensively lay out a plan for a sound system of environmental protection administration. The Environmental Health Division, the Department of Health, Executive Yuan, was upgraded to the "Environmental Protection Bureau," under the leadership of Director Chuang Chin-yuan, to take on the responsibilities of air pollution control and environmental health, the original tasks of the Department of Health, as well as to take over water pollution control and traffic noise control matters that originally belonged to the responsibilities of the Ministry of Economic Affairs and the National Police Agency, respectively. In addition, the Southern Environmental Protection and Surveillance Center was established to manage and execute public hazard control at the national, provincial and inter-city levels. Meanwhile, Director Chuang Chin-yuan actively promoted public hazard control to lay a solid foundation for environmental protection policies and measures as well as for the establishment of the Environmental Protection Administration.
• The Taiwan Provincial Government integrated the Institute of Waste Water Treatment and Environmental Health into the Environmental Protection Bureau, governed by the Department of Health, Taiwan Provincial Government, on August 9, 1983. Taipei City and Kaohsiung City expanded the organization of the Department of Environmental Cleaning and Environmental Administration and reformed them into the Environmental Protection Bureau, on July 1, 1982.
• Since September, 1984, every city and county has designated Section II of the Health Bureau as the responsible agency to manage environmental protection matters.

Stage 4: From August 22, 1987 to August 21, 2023

• On August 22, 1987, the Environmental Protection Bureau, the Department of Health, Executive Yuan, was upgraded as the "Environmental Protection Administration, Executive Yuan " , with Chien Yu-hsin as the Minister. Under it were seven departments: comprehensive planning, air quality protection and noise control, water quality protection, waste management, environmental sanitation and toxic substance management, supervision evaluation and dispute resolution, environmental monitoring and information management. The Taiwan Provincial Government upgraded the Environmental Protection Bureau as the Department of Environmental Protection on January 15, 1988. In coordination with the re-structuring of governmental organizations, the Department was reformed as the Central Taiwan Office in July 1999, and was annexed to the EPA in March 2001 and re-organized as the EPA Inspectorate. Each city and county government gradually set up an Environmental Protection Bureau to enhance environmental protection work and functions between 1988 and 1991. With the establishment of the Environmental Protection Bureau of Lienchiang County, in January, 2003, the environmental protection organization and structure was complete.

Stage 5: From August 22, 2023 to the present

• The Environmental Protection Administration was restructured as the Ministry of Environment, with Shieu Fuhsheng, the former president of National Chung Hsing University, as the minister. At the same time, four tertiary agencies -- the Climate Change Administration, the Resource Circulation Administration, the Environmental Management Administration, and the Chemicals Administration -- along with the National Environmental Research Academy were established. In response to the international trend towards net-zero emissions and other global environmental changes, the government has changed its approach from "management of natural resources" to "actively responding to the global environmental situation and creating opportunities for Taiwan's transformation". This involves integrating expanded authority and systematically dealing with climate change, resource recycling, chemical substance management, management of environmental quality, and strengthening of environmental research.