In an order his lawyer called unprecedented, the Court of Military Commission Review has told both sides to file arguments only on whether the court has the authority to hear the appeal.
"It's terribly unfair to Khadr," Sam Morison, Khadr's American lawyer, who works for the U.S. Defence Department, said in an interview Friday.
"The court's supposed to be neutral. That's what's most troubling."
Normally, appeal courts hear arguments on all the issues at play — including the merits of the case — allowing everything to be decided together.
The military court's new tack, however, could see the case drag on interminably if it decides it has no authority to hear the appeal regardless of its merits.
If that happens, Khadr, 27, would first have to ask a civilian court to order the military court to hear the case, and then, if successful, would have to start from scratch to argue the merits.
The process could take years.
"The practical effect of the court's order is thus to indefinitely postpone meaningful judicial review of the merits of appellant's appeal, thereby ensuring that he will remain in prison unless and until his full term expires," Morison argues in an objection to the court's directive.
"If the government cannot defend the charges it brought against the appellant today, then there is no good reason to believe that it will articulate a winning argument years from now."
The wording of the direction "creates an appearance that the court has prejudged the outcome of this appeal," Morison argues.
Khadr pleaded guilty to five war crimes in October 2010 before a widely maligned U.S. military commission and was sentenced to eight more years in custody.
His lawyers maintain a guilty plea was his only way out of Guantanamo, given that he faced indefinite detention even if acquitted.
The Toronto-born Khadr appealed the convictions Nov. 8, arguing what he was convicted of doing as a 15 year old in Afghanistan was not a war crime under American or international law.
Just days earlier, another former Guantanamo Bay prisoner David Hicks — an Australian charged with providing material support for terrorism — appealed his conviction.
In that case, a panel of the military appeal court directed both sides to file all their arguments — on jurisdiction and merits — at the same time.
However, the U.S. government on Friday moved to stay Hicks's appeal pending the outcome of its fight to have another ruling that quashed a military commission conviction overturned.
Alternatively, the government asked the Hicks panel to issue an order like the one just issued in Khadr's case.
While Khadr appears to have given up his right to contest his conviction under terms of his plea deal, Morison argues military commission authorities didn't follow the appropriate appeal-waiver law.
The various defence arguments are similar to those made by two associates of terrorist mastermind Osama bin Laden. In both cases, a civilian court quashed their military convictions.
The most serious charge against Khadr — murder in violation of the law of war — arose out of the death of an American special forces soldier in the heat of a vicious battle at an Afghan compound in July 2002.
The Canadian citizen is now serving out his sentence as a maximum security prisoner in Edmonton.
Khadr's Canadian lawyers are suing the federal government for breaching his rights. They also want him considered a young offender and moved to a provincial jail.
The federal government, which brands him a dangerous terrorist, has expressed determination to keep him where he is.
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