A court has struck down portions of the National Defence Act that stipulate how military judges are appointed, arguing the lack of security in their tenure denies them the independence required by the Charter to conduct themselves impartially.
The Harper government responded Wednesday by saying it would introduce legislation to rectify the problem.
Military judges are appointed by the government for five year, renewable terms and their job includes trying all Criminal Code offences including murder committed abroad, treason, sedition and spying.
They can be removed from the bench, however, after their half-decade term has ended.
Defence Minister Peter MacKay's office said the government will bring a bill forward to grant judges longer terms.
"It's the government's intention to reintroduce military justice legislation which contains provisions to give military judges tenure until retirement," MacKay spokesman Jay Paxton said.
The Court Martial Appeal Court of Canada ruled unanimously on the matter, arguing in a judgment released June 2 that military judges must be "constitutionally independent of the chain of the command" and the government.
"It seems inconceivable to me ... that military judges who exercise the same functions and have essentially the same powers as superior and provincial courts of criminal jurisdiction, should be subject to the whims, the unknowns, the uncertainty and anxiety of having their positions come up for renewal every five years," Mr. Justice Gilles Létourneau wrote.
The decision has its origins in an appeal by Alexis Leblanc, an enlisted soldier, who was convicted in 2010 of having negligently performed a military duty.
He appealed the verdict, arguing the Standing Court Martial should be declared unconstitutional because military judges appointments, as they stood, did not provide institutional guarantees of independent mandated by the Canadian Charter of Rights and Freedoms. The Charter gives the accused a right to a hearing by an independent and impartial tribunal.