The Maltese National Co-ordination Authority is based at the Office of the Deputy Prime Minister and Minister for European Funds, Social Dialogue and Consumer Protection. The Maltese National Co-ordination Authority oversees two specific functions:

1.  A regulatory function related to the responsibility of the Maltese State as regards monitoring and control of activities, verification of the procedures and expenses of Maltese project partners.

2. A function of coordination of the implementation of the Cooperation Program on Maltese territory and a contribution to the general animation of the program in collaboration with the Managing Authority and the Joint Secretariat to which the Programme Partners entrusted management.