The Federal Government has approved the extradition of an Australian citizen accused of war crimes during the Balkan conflict.

Serbian-born Daniel Snedden, also known as Dragan Vasiljokovic or Captain Dragan, has been appealing against a High Court order in 2010 to extradite him to Croatia.

He is accused of killing, torturing and raping civilians while he was a Serbian paramilitary commander during the conflict.

Home Affairs Minister Jason Clare has now given the green light for Mr Snedden's extradition but the decision can be appealed against

Mr Snedden was held in prison after being arrested by Australian Federal Police in 2006 on request from the Croatian government.

He was released from prison in 2009 when the Federal Court ruled he could not get a fair trial in Croatia.

He went on the run when the High Court approved his extradition in 2010, but was captured by police in New South Wales following a worldwide manhunt.

Mr Snedden is currently being held in a Sydney prison.

Meanwhile, the ruling comes as a UN court has acquitted two Croation ex-generals of war crimes over the 1990s conflict.