At the ceremony, Prime Minister Kosor said that 12 Catholic secondary schools, two primary schools and 48 pre-school institutions were operating in Croatia.
Kosor said that today's agreement was also an encouragement to the endeavours of the Croatian schooling system to preserve Croatia's heritage and identity.
She said that the signing of today's agreement was one of important introductory events ahead of the forthcoming visit of Pope Benedict XVI to Croatia.
The pontiff will visit Zagreb on 4-5 June.
Osijek-Djakovo Archbishop Marin Srakic said that the agreement cites which schools in Croatia are Catholic and regulates their curricula and the sources of their funding.
The dignitary said there was over a one million Catholic schools worldwide.
Catholic secondary schools are in Zagreb, Split, Dubrovnik, Zadar, Pazin, Pozega and Slavonski Brod while the two Catholic primary schools are in Pozega and in Sibenik.