A handful of serious criminal cases — now tied up in the military justice system over questions of constitutionality — likely will be put before a civilian judge after Canada's top court has dismissed an attempt to temporarily stay the effects of a case that has hobbled the courts-martial system.

The Supreme Court of Canada on Monday rejected a motion by the director of military prosecutions to order a stay on the effects of the appeals court ruling involving Master-Cpl. Raphael Beaudry, who was charged with sexual assault but denied a jury trial back in September.

The appeals court ruled in Beaudry's case that the inability of soldiers, sailors and aircrew to elect trial by jury for serious crimes (those punishable by five years or more in prison) amounts to a violation of the Charter of Rights and Freedoms.

The effect on the military justice system has been profound. National Defence says 35 cases have been called into question by the Beaudry ruling.

Most of the cases currently in doubt — 22 — involve sexual assault charges.

Only five courts martial are scheduled to proceed. A dozen are waiting in the wings with no trial date, while another 15 are in limbo.

"We really have an obligation to reassess the cases that we have ongoing and determine whether it would be better for things to be dealt with downtown," said Col. Bruce MacGregor, the director of military prosecutions.

He was unable to say how many cases would be transferred to civilian court, a move MacGregor has resisted in the past because it means the military loses control over how, when — or even if — they're prosecuted.

The military prosecution branch has appealed the so-called Beaudry decision. The Supreme Court won't hear the case until March, however — and military prosecutors wanted to remove the uncertainty by asking that the ruling's effects be suspended.

MacGregor said he respects the court's ruling and will have to deal with the repercussions.

"I'm disappointed because I believe we had a very important position to put forward," he said.

CBC News reported last month that military judges have been opting to adjourn trials until after the Supreme Court rendered its judgment on the constitutionality of the military justice system.

MacGregor said in a written statement early Monday that the issues the Supreme Court was considering would determine the future of the military justice system, which is separate and distinct under law from civilian courts.

He attempted to reassure those in uniform that they remain on top of serious crimes.

"While the court did not grant the motion, I wish to assure the women and men of the armed forces and all Canadians that the military justice system continues to perform its critical role in maintaining the discipline, efficiency and morale of the Canadian Armed Forces," MacGregor said.

"We will continue to consider all possible options to ensure that any impacted cases move forward expeditiously and are prosecuted to the fullest extent of the law."

Military reluctant to turn cases over to civilians

He said he is aware of the stakes for those whose cases are being affected by the uncertainty.

"The interests of victims and survivors remain my highest priority. I will continue to ensure that they are actively informed and consulted in all cases," MacGregor said.

"I also remain mindful of the need to proceed with all cases in a timely manner, and the right of accused persons to be tried within a reasonable time as set out in the Supreme Court decision in the Jordan case."

It is the eighteen month timeline to ensure a speedy trial, in the landmark Jordan case, which concerns military prosecutors.

"There are a number of cases that we will consider on a case-by-case basis for potential transfer to the civilian justice system," said MacGregor. "