Croatian authorities say a dual Serbian-Australian citizen who was a paramilitary commander during the Balkan wars in the 1990s is being extradited to Croatia to face war crimes charges.

Dragan Vasiljkovic, also known as Captain Dragan and Daniel Snedden, was handed over to Croatian authorities at the airport in Sydney Wednesday after losing a 10-year court battle against extradition.

He is accused of killings and torture of civilians while he was a rebel Serb commander during the 1991-95 war.

Serbia-born Vasiljkovic came to Australia when he was 15 but returned to the Balkans to train Croatian Serb rebels in 1991 when Serbs took up arms against Croatia's secession from Yugoslavia.

He has acknowledged serving in the Serb military, but has repeatedly denied committing war crimes during the conflict.