An Australian citizen who was a Serb paramilitary commander during the 1990s Balkan wars is to be deported to face trial in Croatia for war crimes after years on the run.

The Australian High Court upheld Croatia's extradition appeal, ending nearly four years of court battles by the Croatian government and Dragan Vasiljkovic, now known as Daniel Sneddon.

Belgrade-born Mr Vasiljkovic went to live in Australia when he was 15 but returned to his homeland to train Croatian Serb rebels in 1991, when Serbs took up arms against Croatia's secession from the former Yugoslav federation.

The man once known as "Captain Dragan" is accused of instructing others to commit murder and of killing civilians while commanding a Serb paramilitary unit during the 1991-93 Serbo-Croat war.

He acknowledges serving as a Serb commander but has repeatedly denied committing war crimes during the Croatian conflict, which killed about 10,000 people.

In Croatia, the offences carry a maximum penalty of 20 years in jail.