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The investigation and prosecution of sexual-misconduct cases in the Canadian Armed Forces will be moved from the military justice system to the civilian system, following years of calls for such a change.

Defence Minister Anita Anand announced the decision Thursday, in a letter to former Supreme Court justice Louise Arbour. Ms. Arbour is in the midst of conducting a review of sexual misconduct and harassment in the Canadian Armed Forces (CAF) and the Department of National Defence.

Explainer: Which of Canada’s top military officers are accused of sexual misconduct so far? A continuing list

Survivors and legal experts familiar with the Canadian military justice system’s handling of sexual assault have long called for such cases to be dealt with in the civilian system. The government is acting after Ms. Arbour included a move to civilian justice in a set of interim recommendations she sent to former defence minister Harjit Sajjan on Oct. 20. (Ms. Arbour’s final recommendations are expected in the spring.)

Ms. Anand, who was appointed Defence Minister last week, said in her letter that the Defence team would “begin work immediately to implement” Ms. Arbour’s recommendations.

Retired colonel Michel Drapeau, who is now a lawyer and adjunct professor of law at the University of Ottawa, said Thursday that he has argued in favour of handling military sexual misconduct in the civilian justice system for at least a decade. He called Ms. Anand’s decision a “welcomed sign of leadership.”

“This is a game-changer decision,” he said. “This ministerial decision sends a timely and powerful signal to the military justice system and victims that changes are coming.”

In her recommendations to Mr. Sajjan, Ms. Arbour noted allegations of sexual misconduct against senior CAF leaders. She wrote that related probes by the Canadian Forces National Investigation Service, which is the investigative arm of Canada’s military police, have led her to conclude that “immediate remedial actions are necessary” to restore trust in the Forces.

Sexual misconduct in the military has been an ongoing concern for the past several years. Recently, allegations against high-ranking officials have added urgency to calls for reform. The Canadian Forces National Investigation Service probed sexual-misconduct allegations against former chief of the defence staff Jonathan Vance earlier this year. Mr. Vance’s successor in the role, Art McDonald, stepped down in February after a separate sexual-misconduct allegation. Neither man faced charges in those cases, though Mr. Vance was separately charged with obstruction of justice.

Canada’s military justice system operates in parallel to the civilian criminal justice system. The military system is established within the Code of Service Discipline, which is part of the National Defence Act.

The Canadian Armed Forces says the military justice system is designed to maintain discipline, efficiency and morale in the military. Sexual misconduct in the Forces did not fall under this system until 1998. Experts have long argued that the civilian system is better suited to dealing with sexual offences because it is more experienced with those types of allegations, and more efficient.

In her interim recommendations, Ms. Arbour said she believed it necessary to establish a process that would facilitate the handling of sexual-offence allegations in an “independent and transparent way,” outside the CAF’s chain of command. She called for the implementation of a recommendation made in June by another former Supreme Court Justice, Morris Fish, who, in his own review of the National Defence Act, also argued for sexual assaults and other criminal offences that are sexual in nature to be referred to civilian authorities. The move was also among the recommendations in a third independent report, written in 2015 by former Supreme Court justice Marie Deschamps.

Ms. Arbour added that The Canadian Forces Provost Marshal should not only transfer future allegations of sexual offences to civilian authorities, but also offences currently under investigation by military police, unless those investigations are nearing completion.

“In any event, in all cases charges should be laid in civilian court,” she wrote.

In a statement Thursday, Ms. Arbour welcomed Ms. Anand’s decision to accept the interim recommendations.

“The issue of sexual misconduct in the CAF has opened the institution to unprecedented scrutiny and an equally unprecedented opportunity for change,” Ms. Arbour said. “I will continue as part of my review to identify these opportunities in all the areas that fall within my mandate.”

Elaine Craig, a professor at the Schulich School of Law at Dalhousie University in Halifax, said it is clear that Ms. Anand takes seriously the “endemic problem of sexualized violence in the Canadian Armed Forces.”

Survivors of military sexual trauma in Canada and legal experts familiar with the Canadian military justice system’s handling of sexual offences have called for civilian justice for years, she said.

“While also flawed, the civilian legal system’s prosecution of sexual offences is more efficient, more experienced and far less expensive,” Prof. Craig said. “It is entirely appropriate to return exclusive jurisdiction over these offences to civilian courts, given the failures of the military to adequately respond.”

In her 2015 report, Ms. Deschamps noted the need for a way of handling sexual-misconduct allegations outside of the chain of command.

She highlighted how other parts of the world – such as the U.S., Australia and France – have created independent offices to receive reports of sexual misconduct in their militaries. Her review also determined that victims tend not to report sexual assaults to the military justice system, because they fear being mistreated by it.

In order to rebuild trust in the system, she said in her report, complainants need to know that the CAF is committed to ensuring their allegations are properly investigated. This could be achieved, Ms. Deschamps wrote, in part by “allowing the victim to request to have her case transferred to civilian authorities.”

Mr. Fish told The Globe and Mail that a move to civilian justice in military sexual misconduct cases was a core recommendation in a chapter of his report. The government’s decision to implement it indicates Ms. Anand’s resolve to act promptly on Ms. Arbour’s interim recommendations, he said.

“This tends to eliminate any concern that the implementation of my other urgent recommendations will be postponed until after Justice Arbour completes her review and produces her own final report,” he said.

Conservative defence critic James Bezan said that the Liberal government has failed to implement recommendations on the sexual-misconduct crisis in the military in the six years since Ms. Deschamps’s recommendations. Prime Minister Justin Trudeau, he added, “must immediately tell our brave men and women in uniform and all Canadians when and how today’s policy will be implemented.”

NDP defence critic Lindsay Mathyssen said that Mr. Trudeau and his government had ignored the recommendations in Ms. Deschamps’s report. “It should not have taken this long to make this change,” she said.