The following structures for the management of the Programme have been set up:
| Programme Implementing Body | Responsible Institution | |
|---|---|---|
| Managing Authority (MA) | Ministry of Foreign Affairs and Trade of Hungary, Budapest | |
| National Authority (NA) | Ministry of Regional Development and EU Funds of the Republic of Croatia, Zagreb | |
| Certifying Authority (CA) | Hungarian State Treasury, Budapest, Hungary | |
| Audit Authority (AA) | Directorate General for Audit of the European Funds, Budapest, Hungary. | |
| Joint Secretariat (JS) | In Budapest and Pécs (Hungary), hosted by Széchenyi Programme Office Nonprofit Ltd. (SZPO) | |
| JS Contact Points | In Osijek and Čakovec (Croatia) | |
| Control Bodies | Hungary | Széchenyi Programme Office Nonprofit Ltd. |
| Croatia | Ministry of Regional Development and EU Funds of the Republic of Croatia, Zagreb | |
Monitoring Committee (MC) is the decision-making body which supervises and monitors the Programme implementation.
