The Joint Technical Secretariat performs functions of the Joint Secretariat of the Interreg V-A Lithuania–Poland Cross Border Cooperation Programme as well as Joint Technical Secretariat function of the 2014-2020 European Neighbourhood Instrument Cross-border Cooperation Latvia-Lithuania-Belarus and 2014-2020 European Neighbourhood Instrument Cross-border Cooperation Lithuania-Russia Programmes.
The Joint Technical Secretariat is also hosting the branch offices of the Interreg V-A Latvia-Lithuania and Interreg South Baltic Programmes.