"Croatia can prosecute war crimes and those who committed crimes on the Croatian side," said Mesic during an interview in Berlin to coincide with the 10th anniversary of the US-brokered Dayton accords which stopped the killing in the former Yugoslavia.
"Partiality is now excluded. Croatia is implementing the reform of the judiciary," said Mesic.
Mesic also said he was confident that domestic courts were "completely impartial" in trying alleged war criminals.
"The Croatian judiciary was not impartial in the past," he said. "There was a selective application of laws on our country. The laws were implemented in respect to some peoples but not in respect to other persons," Mesic said for International Herald Tribune.
When asked if it was the Serbs whom the courts were partial against, he said "Yes, it was the Serbs."
"I wish the Hague would complete its work," said Mesic, expressing a view shared by many Croats, for whom the tribunal represents a dark reminder of their past and their country's role in the war crimes.
Mesic acknowledged that Croatia had been slow to cooperate with the Hague tribunal, the newspaper said.
International Herald Tribune said that the EU had considerable doubts that the courts in Croatia could be sufficiently impartial to hold war criminal trials.
The paper also said that the commission pointed out that "the vast majority of these cases had been against Serbs, with little appetite to try Croats and many cases have been tried in absentia as well as based on unsubstantiated evidence.