A Serbian war crimes suspect known as "Captain Dragan" was handed over by Australia to Croatia Wednesday to face allegations of torture and murder after battling extradition for a decade.

Dragan Vasiljkovic, a paramilitary commander with a Serbian rebel group opposed to Croatia breaking away from Yugoslavia, is wanted on charges relating to Zagreb's 1991-1995 war of independence.

The Belgrade-born 60-year-old, who has Australian citizenship, has previously denied committing war crimes but told media he trained recruits, killed in combat and interrogated enemy troops.

Canberra approved his extradition in 2012 and The Australian newspaper, which first revealed his identity in 2005, said he would be put on a plane in Sydney on Wednesday for Croatia.

The Australian Attorney-General's Department confirmed he had been "surrendered to the Republic of Croatia pursuant to an extradition request made in 2006".

"Criminal proceedings against Mr Vasiljkovic in Croatia are a matter for Croatian authorities," it added in a statement.

Vasiljkovic is the first accused war criminal Australia has successfully extradited.

Lawyer Darko Stanich told Australia's SBS radio that a court in Split had appointed him to represent Vasiljkovic, known as Daniel Snedden in Australia, and he expected to meet him on Thursday after his transfer from Sydney to Zagreb.

"The fact is that he is the first Australian citizen to be extradited to another country, for now, without final judgement," he said.

"If he is imprisoned it doesn't mean that he is truly guilty. Whether guilty or not will be determined through a judicial process."

Vasiljkovic was first arrested in Australia in 2006 after Zagreb requested his extradition and he spent nearly four years behind bars until the Federal Court blocked his surrender over possible prejudice in Croatia's justice system.

He was released on bail in September 2009 but went missing the following March, after a court cleared his extradition to face Croatian justice.

He spent more than 40 days on the run before police tracked him down to the New South Wales north coast and sent him to a Sydney prison. He has been battling the extradition request from there until a few months ago, The Australian reported.

The Australian, which has run a long campaign to expose war crimes suspects, said Vasiljkovic faced three allegations, including reports that he commanded troops in 1991 from the so-called Red Beret brigade, the Kninjas, who tortured and killed prisoners of war.

He is also accused of commanding a deadly assault on the town of Glina in which civilians were killed, and committing breaches of the Geneva Convention during an assault by his troops at the town of Bruska near Benkovac.