The support and reimbursement of salary expenditure of the administrative capacity of the Managing Authority for the Operational Programme Technical Assistance (RO OP TP), the Department of Administrative Capacity of the ESI Funds (ESIF AK), the Payment Unit for the Operational Programme Technical Assistance (OPTP) involved in the system of management and implementation of the ESI Funds in the 2014-2020 programming period at the level of the Slovak Republic’s Partnership Agreement for 2014-2020 (PD SR) is an essential precondition for achieving efficient and effective management and implementation of ESI Funds. According to Slovak Government Resolution No 519/2014, the MA OP TP, PJ OP TP, AK ESIF in the 2014-2020 programming period perform the tasks of the Slovak Government Office. The National Authority and the National Contact Point for Transnational Cooperation Programmes and European Territorial Cooperation is involved in the system of management of the European Structural and Investment Funds at the level of the Slovak PD. The European Territorial Cooperation Programmes Interreg Central Europe 2014-2020 and Interreg Danube transnational programme 2014-2020 have an important role to play in defining the areas to be assisted under the new operational programmes of the PD SR. The Government Office of the Slovak Republic is the body responsible for the preparation and implementation of transnational cooperation and European territorial cooperation programmes within the meaning of Slovak Government Resolution No 604/2013. Slovak Government Resolution No 318/2014 approved the Central Europe 2020 Cooperation Programme and Slovak Government Resolution No 34/2015 approved the Danube Transnational Programme 2014-2020. Support for the administrative capacity of the National Authority and the National Contact Point for transnational cooperation and European territorial cooperation programmes in the 2014-2020 programming period is a prerequisite for achieving effective preparation and implementation of transnational cooperation programmes.