But a war crimes expert and a former Hague prosecutor said domestic courts like those in Bosnia are now the only practical place to run such cases.

Former Bosnian Croat soldier Krunoslav Bonic, 39, is facing extradition from the ACT, where he has lived for up to a decade, to face allegations of war crimes against civilians in Bosnia.

The allegations stem from the bloody 1992-95 Bosnian war involving the country's Serb, Croat and Bosniak Muslim ethnic groups.

But the Bosnian court system where Bonic could be tried has received mixed assessments in recent years.

Transparency International, an anti-corruption organisation, described the Bosnian judicial system as poorly resourced and backlogged with cases, finding it was widely perceived as corrupt by Bosnian citizens.

The group, in a report published last year, found the courts were often the subject of pressure from the country's different political and ethnic groups, particularly over war crimes cases.

It ranked the judicial system as weak, giving it a score of 29 out of 100, mainly deducting points for its lack of action to combat corruption in the country.

But others have expressed confidence in the Bosnian courts' ability to deal with war crimes cases.

The Organization for Security and Co-operation in Europe and prosecutors at The Hague's International Criminal Tribunal for the former Yugoslavia found in 2011 that cases being transferred to Bosnian courts were being dealt with in line with international and national standards.

Significant investment and training was made to help develop the Bosnian justice system in the wake of the war to ensure such crimes were tried fairly and effectively.

Flinders University academic and former Hague prosecution team member Grant Niemann said the domestic courts are now the only practical place to try cases like Bonic's, given Australia's reluctance to prosecute and the winding up of the Yugoslavian war crimes tribunal.

Dr Niemann, who had little to do with Bosnian courts during his time at The Hague, said he understood the country's system to be genuinely trying and improving.

He said the reasonable rate of acquittals for war crimes in the country suggested they were trying cases fairly.

"There doesn't seem to be too much evidence of them taking out revenge," he said.

"If you say 'is it as good as The Hague?', no probably not, 'is it as good as Australian courts', no probably not.

"But this is not an isolated situation, there are courts all over the world which are not as good as those."

Bonic's case will return to the ACT Magistrates Court next month.

He is in custody and will take his first and only shot at bail in late November.