Captain Dragan Vasiljkovic, also known as Daniel Snedden, has been fighting extradition to Croatia for almost a decade.
The New South Wales Department of Corrective Services has confirmed he was taken from Sydney's Parklea prison and put on a flight to Croatia.
This afternoon the Federal Attorney General's department confirmed to SBS that Vasiljkovic had been surrendered to Croatia.
"On 8 July 2015 Mr Dragan Vasiljković, a dual Australian-Serbian citizen, also known as Daniel Snedden, was surrendered to the Republic of Croatia pursuant to an extradition request made in 2006," the statement read.
Several news organisations in Croatia are reporting that Mr Snedden, who had been held in extradition detention in Sydney, was expected to land in the Croatian capital Zagreb on Thursday (evening AEST).
Lawyer Darko Stanich said a court in the southern Croatian city of Split had appointed him to represent the 60-year-old Australian, who denied the charges against him.
Mr Stanich told SBS Radio's Croatian program expects to meet Mr Vasiljkovic in Split on Thursday, and if he doesn't decide to appoint new lawyers, he'll represent him like any other client - as an innocent man until proven guilty.
"The fact is that he is the first Australian citizen to be extradited to another country, for now, without final judgment," 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. However, according to my information, he is already more than eight or nearly nine years in extradition detention in Australia without a final verdict."
Croatia wants to try Mr Snedden on three counts of alleged involvement in war crimes during the Balkan conflict in the 1990s.
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