Croatia has set up a centralised control system. In centralised control systems, a central body is appointed to carry out the national controls in accordance with article 46. (3) of the ETC Regulation No 2021/1059 and with reference to article 74. (1 and 2) of the CPR Regulation No 2021/1060.

The control tasks are carried out by the National controllers (ex-first level controllers), permanently employed staff contracted by the Ministry of Regional Development and EU Funds (MRDEUF). The National controllers are responsible for verifying the legality and regularity of the expenditure declared by each lead beneficiary and/or project partner participating in the project located on its territory. Following the completion of the control, Control Body issues NC Certificate on the eligible and validated expenditures to the lead beneficiary/project partner.