Daniel Snedden, formerly known as Dragan Vasiljkovic, was in command of a Serb paramilitary unit during the war in Croatia in the early 1990s and has been accused of beating a prisoner of war.

It is also alleged he was in charge of others who mistreated prisoners over nearly two months, which resulted in some deaths.

Justice Cowdry rejected claims that Snedden would be unfairly tried in a judiciary biased against Serbs.

"The court is not satisfied that the evidence establishes that there are substantial grounds for believing that the applicant may be prejudiced at his trial," said Justice Cowdry in delivering his judgment.

Despite a 12-year delay surrounding the start of the investigation, Justice Cowdry ruled that any argument relating to an abuse of process was a matter for the Croatian judiciary, not the Federal Court.

Justice Cowdry also dismissed Snedden's claim that he could not be guaranteed a jury trial in Croatia, as he had not been charged with Commonwealth offences

Snedden can seek leave to appeal to the full bench of the Federal Court and also directly to the Attorney-General not to be deported.

- Sarah Sharples