The General Strategy Department deals with the co-ordination of preparation and implementation of long-term and medium-term programmes, determines their priority and supervises their implementation. It also prepares drafts of laws and decisions taken by the government, prepares standards, co-ordinates environmental education, the implementation of economic measures, handles projects management, participates in international co-operation and co-ordinates the EU integration process.

The Department of Environmental Quality sets up and controls emission standards and is in charge of issuing permits to control the emission of pollutants and radioactive substances into the environment. It supervises the import, transit, export, use, handling, disposal and treatment of hazardous chemical and radioactive substances and sets standards of radioactive safety. In preparing recommendations and issuing directives and standards to improve the quality of the environment, Lithuania is following the strategies of two main institutions: the Helsinki Commission and the Commission of the European Communities.

The Department of Land Management and Biological Diversity organizes and issues new strategies, programmes and directives on territorial planning in order to conserve the landscape and biological diversity. The main measures taken include the establishment of a system of protected areas (strict reserves, reserves, national and regional parks, etc.), the implementation of maintenance and other measures in these areas and the compilation of the Red Data Book (in which all endangered species are listed). The MEP administers four strict nature reserves: Cepkeliai, Kamanai, Viesvile and Zuvintas, as well as the Curonian Spit National Park, with its unique dunes, and 14 regional parks.

The Joint Research Centre, which is subordinated to the MEP, started a complex monitoring of the environment in 1950-65. It collects detailed data on environmental change carries out environmental impact studies, provides information, recommendations to the state, local government on the environmental management and the rational use of natural resources.

On the international level, MEP has signed agreements with almost all the states in the Baltic region, and several other European countries, on environmental protection.