The court martial for Canada's chief military judge is in limbo after the judge overseeing the trial — who happens to be deputy to the accused — agreed not to hear the case over conflict-of-interest concerns.

Lt.-Col. Louis-Vincent d'Auteuil also outlined the reasons why he felt the military's other three sitting judges would not be able to preside over Col. Mario Dutil's trial in an impartial manner.

That has left the fate of Dutil's court martial, seen by some as a critical test for the military-justice system, up in the air.

"I met briefly with the prosecutors and asked them to inform me formally as to what the intent is," Dutil's lawyer, Philippe-Luc Boutin, said Tuesday. "So I don't know. We're just in limbo and waiting for the prosecution to make a decision."

Military prosecutor 2nd Lt. Cimon Senecal said he was weighing his options, but remained committed to pressing ahead with the case.

"At this point, the public interest for these charges to proceed is higher than it has ever been," Senecal said in an email.

"The special prosecution will do everything in its power … to ensure Col. Dutil responds to these charges. There are options and we are in the process of determining which one is the most appropriate."

Dutil was charged with eight counts in relation to allegations he had an inappropriate relationship with a subordinate and knowingly signed a travel claim for $927.60 that contained false information.

Four of the charges were dropped at the start of the court martial last week, where Boutin served d'Auteuil with a subpoena before challenging the presiding judge's impartiality and asking him to recuse himself.

A publication ban on details of that portion of the hearing, which included Dutil testifying about his relationship with d'Auteuil, whom he described as a "confidant," has since been lifted.

In a decision written in French agreeing to Boutin's request, d'Auteuil said it was reasonable for observers to believe he would be biased because of his relationship to several potential witnesses who are employees of the court.

"It has been shown that a well-informed person who studied the question in depth, in a realistic and practical way, would conclude that because of the existing links between certain court stenographers and myself, I would be biased," he wrote.

He added that he did not feel he could appoint one of the military's other three judges to take his place because they either had similar ties to the witnesses or didn't have the right language skills or expertise for such a complex trial.

Dutil also had an acrimonious relationship with one of the three judges, which d'Auteuil said was another reason not to appoint that judge to preside over the court martial.

"Public confidence in the court-martial system and the function of a military judge could be undermined if I appoint a replacement military judge from among those who are currently eligible," d'Auteuil concluded.

Despite d'Auteuil's decision, Senecal said he stood by the decision to press forward with a court martial rather than send the case through a civilian court, adding: "We are still confident that we will find a way to serve justice in this case."

But Boutin believed it was obvious from the start that the military-justice system would have a difficult time handling the case, and that "this long process could have been avoided."

Prosecutors could try to get a reserve military judge, Boutin said, or send the file to the civilian system where Crown prosecutors would have to weigh whether it was feasible and in the public interest to move ahead with a trial.

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