"I was in transit, the checking of my documents was lasting for a long time and when I asked what was going on ... I was told that there was an arrest warrant that was still valid," Haradinaj told AFP over the phone.
"Now they want me to appear before a Slovenian court to clear this up. Why would I appear in court here? .... They are (the Slovenian authorities) the ones who messed up," he said.
Meanwhile, Serbian state-run RTS television reported that the warrant for Haradinaj, a former commander of the Kosovo Liberation Army (KLA) -- a pro-independence ethnic Albanian rebel movement -- was issued in 2006. It did not provide any other detail.
Haradinaj was returning from Germany and was waiting at the Slovenia's capital airport for a flight to Pristina.
More From This Section
The government voiced "concern that such warrants are still treated as valid in certain countries, despite the fact that ... Haradinaj's innocence was proven ... By the international justice," a statement said.
Meanwhile, Haradinaj's Alliance for the Future of Kosovo (AAK) called for an "immediate action" to allow him to continue his return to Pristina.
During the 1998-1999 war KLA guerrillas fought the armed forces of then Serbian strongman Slobodan Milosevic.
The war ended when a NATO-led air campaign halted Milosevic's crackdown on the pro-independence Kosovo Albanians and ousted his forces from the territory in June 1999.