The functions of Intermediate Bodies are performed by:
Ministry of the Environment (MoEn) – in the field environment protection;
Ministry of Transport (MoTC) – in the field of transport infrastructure development;
Ministry of Economy (MoE) – in the fields of enterprises and industry, energy and tourism development;
Ministry of Social Security and Labour (MoSSL) – in the field of social integration;
Ministry of Education and Science (MoES) – in the field of human resources development;
Ministry of Healthcare (MoH) – in the field of healthcare;
Ministry of Agriculture (MoA) – in the fields of agriculture, rural development and fisheries;
Information Society Development Committee (ISDC) under the Government of the Republic of Lithuania – in the field of information society development.

The functions of Implementing Agencies are performed by:
Environmental Projects Management Agency (EPMA) of the Ministry of Environment for environmental projects;
Transport Investment Directorate (TID) for transport projects;
Lithuanian Business Support Agency (LBSA) for business development, energy and tourism projects;
Support Foundation European Social Fund Agency (ESFA) for social integration and human resources development projects; National Paying Agency (NPA) under the Ministry of Agriculture for agricultural, rural development and fisheries projects;
Central Project Management Agency (CPMA) for infrastructure projects in the fields of healthcare, education and science and social protection, for information services development and technical assistance projects.