Some French media have recently reported that Gotovina is hiding in south-east France with the help of former legionnaires.
"I have seen unchecked information about General Gotovina, who is at large. I can clearly confirm that he is not on the French territory," AFP quoted ministry spokesman Jean-Francois Bureau as saying.
"We do not know where he is, and operations ICTY chief prosecutor Carla Del Ponte has been conducting to find those who should appear before the ICTY show certain effectiveness. We are making a contribution on our part," Bureau said.
Last week, the Foreign Legion claimed that it had never protected Gotovina although he had served "honorably and loyally" in its ranks 27 years ago.