The Environmental Protection Agency (EPA) was established in 1 January 2003, by the Order of the Minister of the Environment of the Republic of Lithuania No. 466 of 30 August 2002. EPA was established in a way of restructuring and merging former Joint Research Centre and Water Resources Department of the Ministry of Environment. Recently, on January 1, 2006, the activities of the management of chemical substances and preparations were shifted from the State Non Food Products Inspectorate under the Ministry of Economy to EPA, and new Chemical Substances Department with functions to implement these activities was established.

As stated in National Environment Monitoring program The Environment research department performs different types of environment quality examination: air, water, water objects (rivers, lakes) ground, natural ecosystems studies; also performs national level research on pollutant emissions and environment pollution in extreme situations.