In an interview with the Danas weekly, Mesic said Gotovina was too intelligent to risk being caught by trying to hide out in either country.
"We must assure our friends that we have done everything in our power, absolutely everything, and that we are cooperating fully. And we cannot arrest Gotovina because he is not in Croatia," he said.
Croatia's bid to join the European Union was put on ice last month because of concerns in Brussels the Croatian government was not doing enough to capture Gotovina.
Gotovina is widely regarded as a national hero in Croatia for his role in defeating the Serbs during the Balkan wars of the 1990s.
However, he is wanted by the international court in The Hague on suspicion of crimes against humanity.