"Our view has always been that if we were to return Mr Hicks and Mr Habib to Australia there are no charges that we would be able to bring against them under our law as it was at that time," Mr Ruddock told ABC radio.
"There would be under our law as it is now, but there wasn't in terms of our law at that time."
Mr Ruddock said Major Mori was just doing his job as Hicks's lawyer by criticising the American military tribunal system.
"It says that he is giving Mr Hicks the best defence that he can and one of the ways in which defence lawyers often put their case on behalf of their clients is to advocate about the nature of the system which is dealing with them," he said.
Mr Ruddock said it was appropriate for the US to use military commissions to try suspects who had committed crimes during the War on Terrorism.
"Military commissions have been the normal way in which matters that require a trial (are) addressed," he said.
"They are part of the American system, they have certainly been used in an Australian context where we are trying people who have committed offences in a war situation."
Hicks is yet to be charged with any offence.
Major Mori later told Sydney radio 2UE that he did not understand Mr Ruddock's reasoning.
"David Hicks has never injured any US citizen or service member. Why is the US holding him to try him?" Major Mori said.
"If he hasn't violated his country's laws, to the country he owes allegiance, if he hasn't violated any of their laws, why is he being criminally held responsible for anything?"
He said if Hicks had to be tried, he should be tried in a military commission in Australia.
"I know Australia has done those types of military commissions in the past," he said.
The executive order by which George Bush created the military commissions is dated 13 November 2001. It is retrospective with respect to offences committed before that date. In any case, the Australian parliament has power to make retrospective laws and could easily authorise trial by military commission or otherwise in Australia.
What the Australian parliament could not do is oust the power of the High Court to review any military commission's decisions for jurisdictional error. The US Supreme Court has not yet decided the jurisdiction issue in the USA. In any case, Australian law already provided for the offence of treachery. Sadly the Australian government did not bother to activate that offence with respect to the Taliban or al-Qa'ida.
Ruddock's position on retrospectivity is as ingenuous as his earlier claims that the military commission process is fair. And why are the British Guant�namo detainees to get different treatment from the Australian detainees?
Lastly, it's simply untrue (Ruddock, himself a lawyer, knows this) to say that lawyers frequently question the process by which a defendant is tried. In most jurisdictions that is known as contempt of court.