Taiwan Provincial Government upgraded the Environmental Protection Bureau to the Department of Environmental Protection on January 15, 1988. In coordination with the re-engineering of governmental organizations, the Department was reformed as the Office of Central Taiwan in July 1999 and was annexed to the EPA in March 2002 and reorganized as the EPA Inspectorate. Its main responsibilities include promoting general waste management policies, supervising general waste treatment facilities, inspecting environmental pollution cases, and investigating environmental crimes.

Moreover, since the 1980s, Taiwan has been facing the issue of soil and groundwater pollution caused by the improper treatment of industrial wastewater, waste, and air pollution. Therefore, the Ministry of Environment (formerly known as the Environmental Protection Administration, Executive Yuan) developed environmental regulations related to soil and groundwater. The Soil and Groundwater Pollution Remediation Act was promulgated by the President on February 2, 2000, Taiwan established the Soil and Groundwater Remediation Fund.

The Bureau of Environmental Inspection broke the existing organizational framework and established the Northern, Central, and Southern Centers of Environmental Management on January 1st, 2022, in accordance with the principles of "streamlining the organization,", "increasing administrative efficiency,", "establishing a dynamic government,", "promoting policy formulation and implementation,", and "restructuring existing resources, enhancing waste processing capacity, and creating a high-quality environment.".

The Legislative Yuan passed the "Organization Act of the Environmental Management Administration, Ministry of Environment" on May 9th, 2023, and it was promulgated by the President in the same year. The Environmental Management Administration (EMA) upholds the implementation of the President's policy agenda, focusing on introducing the concept of regional environmental governance, promoting digital technology and intelligent management, establishing proper waste disposal practices, unifying the authority for policy and legal enforcement, constructing livable cities with a high-quality environment, implementing people-centric cleanliness and care, and ensuring the sustainable management of soil and groundwater.