Alleged Australian war criminal, Daniel Snedden, better known as Dragan Vasiljkovic or Captain Dragan, is facing imminent extradition, after the High Court rejected his latest appeal bid.

Snedden, who has been accused of three counts of war crimes in 1991 and 1993 during the Balkans conflict, will be handed over to Croatia unless the Australian Government intervenes.

In November 2012, former federal justice minister Jason Clare approved the Australian citizen's extradition and the Federal Court backed that ruling in December.

Snedden applied for leave to appeal in the High Court, arguing the approval was improper based on procedural fairness and sections of the Geneva convention.

However, the High Court has ruled the appeal would be unlikely to succeed and has refused leave to appeal.

It was the last option left to Snedden through the courts.

The only thing now standing between him and extradition is an about face by current Justice Minister Michael Keenan.

His lawyer, Daniel Mori, appealed to Mr Keenan to ensure Snedden received credit for nine years he had already spent in jail in Australia if he was sentenced in Croatia.

"I think any Australian would want that for their family member," Mr Mori said.

Mr Mori also wanted the Government to ensure his client's safety.

"The UN Human Rights Committee just came out last month with a report about the overcrowding of Croatian prisons, of a lack of healthcare provided and that's a serious issue," he said.

Mr Mori said he had already briefed lawyers in Croatia about Mr Snedden's case and hoped DFAT would ensure he had access to lawyers if he was extradited.

The Federal Government released a statement indicating it would follow through with the extradition.

"The Australian Government does not comment on operational matters, including the timing or logistics for surrender," a spokesperson for Attorney-General George Brandis said.

"This is to ensure the safety of all persons involved and to uphold the integrity of the surrender process."

Snedden accused of torture, war crimes

It is alleged Snedden was a paramilitary commander for the ethnic Serbs who were involved in a conflict with the Croatian armed forces.

His men are accused of committing war crimes, including torture, murder and conducting mock executions.

Snedden is alleged to have ordered paramilitary units to fire on a church, a school and homes, while his soldiers have been accused of looting homes after the attack.

Croatia originally applied to extradite him in 2006.

He has been held in a Sydney prison for most of the time since then, without charge.

His latest appeal was on two grounds, the first was that he was denied procedural fairness when he was not allowed to respond to material provided by Croatia to Australia in support of his extradition.

Mr Mori also argued his client could not be handed over unless Croatia first made a prima facie case against him, under article 129 of the Third Geneva Convention.

He said Croatia provided no details of the allegations against his client, and was not required to do so under the Australian Extradition Act.

"It's shocking and I think this case represents some of the flaws in the Australian Extradition Act itself," he said.

"Australia, in protecting its citizens, you'd hope would require a country to provide some evidence that you did something wrong abroad.

"That's what the Geneva Convention says in black and white. Unfortunately it's not part of [Australia's] extradition act."