The U.S. Court of Military Commission Review ruled last month that Khadr could face murder and terrorism charges at a military tribunal at the U.S. naval base in Cuba, overruling an earlier dismissal of the charges.
The trial judge, Col. Peter Brownback, had thrown the case out in June, saying he lacked jurisdiction to try Khadr because the 21-year-old hadn't been declared an "unlawful" enemy combatant as required by Congress.
But the military review panel decided Brownback has the authority to determine whether or not Khadr was legally fighting U.S. soldiers in Afghanistan.
Khadr's lawyers say two e-mails from Brownback to lawyers involved in the case show the determination will be a hasty, sketchy process that's "fundamentally unfair."
That process would bar an appeal about Khadr's status to a regular U.S. court, said Lt.-Cmdr. William Kuebler, and there would be no chance to contest his status until after the military tries him and imposes a sentence.
The defence isn't entitled to all the evidence against Khadr, said Kuebler, and the judge has already said he won't accept arguments that Khadr was an alleged child soldier deserving of international legal protections.
He was 15 years old when he allegedly threw a grenade that killed a U.S. medic in an Afghanistan firefight in 2002.
"The courts in this process seem determined to avoid the most controversial aspect of Omar's prosecution - whether imposing a life sentence on a child for so-called war crimes is legal," said Kuebler.
"Allowing the military commission to decide whether it can legally try Omar is like letting the fox guard the henhouse."
The case, which has faced one legal twist after another, is scheduled to resume Nov. 8 in Guantanamo.
The U.S. military is anxious to try Khadr and is seeking a life sentence.
It would be the first full test of a special justice system for foreign terror suspects initially set up by President George W. Bush and revamped by Congress last year.
The process has been condemned by many western countries and human rights groups, but Canada hasn't criticized it. The Conservative government has said it won't get involved.
Khadr is the only western prisoner left among Guantanamo's 340 detainees. Other countries, like Britain, demanded their citizens be returned home.
Last month, Liberal Leader Stephane Dion urged Prime Minister Stephen Harper to demand that Khadr be tried in a U.S. civilian court or sent home to face justice.
"It's stunning that Canada can continue to be idle in the face of such an affront to the rule of law," said Kuebler.
"In the military commissions, if you're right on the law, they just don't let you make the argument."
Khadr's case could be further complicated by the U.S. Supreme Court. It has agreed to hear arguments about whether Guantanamo prisoners should be allowed to appeal their detentions in a U.S. civilian court.
The hearing will likely be held in December.