Perkovic, who held a leading position in the Yugoslav secret service UDBA until 1991, is also suspected of trying to talk a Croat living in Germany into assassinating two Croatian political emigrants in 1977.
The BKA believes that Perkovic, born in 1945 in Licko Novo Selo, is in Croatia, and has offered a EUR5,000 reward for information leading to his arrest.
In July this year German police arrested Croatian national Krunoslav Prates in connection with the murders of former INA oil company director and novelist Stjepan Djurekovic and emigrant politician Ante Djapic.
The case was covered by the media of the Croatian emigrant community, including the Croatia Herald, which said that Perkovic's son Sasa was working as a national security adviser to President Stjepan Mesic.
Croatian Interior Ministry spokesman Zlatko Mehun told Hina on Thursday that they had seen a notice on the Internet site of the German office, and added that the Interpol office in Zagreb had no information for now about the arrest warrant for Josip Perkovic.
Citing the Croatian constitution, Mehun said that Croatian citizens could not be extradited, and added that it was possible for the Croatian judiciary to take over prosecution from the German authorities.