The two heads of state met ahead of a summit of Central European presidents which Brno is hosting until Saturday.
"The topic was Kosovo and President Mesic said that (UN mediator Martti) Ahtisaari's plan was essential in the process of reaching a solution to Kosovo's final status," said Danijela Barisic, spokeswoman for Mesic's office.
She added the two officials also discussed the situation in Serbia following the formation of the new government, and the return of ethnic Serb refugees to their prewar homes in Croatia.
On the fringes of the Brno summit, Mesic will hold a series of bilateral meetings, including one with Italian President Giorgio Napolitano.