Fresh allegations of war crimes and coverup levelled at Canadian military police and commanders in Afghanistan and in Ottawa are now under investigation by an independent watchdog.

The Military Police Complaints Commission announced Thursday it was conducting a public interest investigation into allegations Canadian military police members abused and "terrorized" Afghan detainees held in a Canadian prison at Kandahar Airfield.

The complaints commission is also investigating why the military's supposedly independent police unit, the National Investigation Service, didn't lay charges in the case, even though it was within the team's power and mandate.

Instead, the complaints commission revealed in a letter, the police unit allegedly deferred to the Canadian commander in Afghanistan, then Brig.-Gen. Dean Milner.

"Charges were allegedly provided to the Canadian Armed Forces (CAF) Task Force Commander who, according to the complainant, ignored them," commission chair Hilary McCormack wrote in a decision letter released Thursday.

Anonymous tip

The allegations were made to the complaints commission in a one-page typewritten letter that was sent anonymously in February from an airport hotel in Toronto.

The complaint alleges MPs ran a series of military training exercises inside the Canadian detainee holding facility at Kandahar Airfield in order to "terrorize" the detainees.  

In at least one incident, it's alleged, the MPs entered a cell holding some Afghan detainees, pressed them up against the wall and floor and twisted their arms behind their backs in so-called arm locks.

AFGHANISTAN/

Three captured Taliban insurgents are presented to the media in Ghazni province, Afghanistan, in August 2011. (Mustafa Andaleb/Reuters)

"The complainant alleges the tension was so high after the previous two months that several detainees defecated and urinated on the spot," McCormack wrote in her letter.

The incidents were investigated by the National Investigation Service, which was set up outside the chain of command in order to preserve its integrity and maintain distance from the influence of the military chain of command.

But no charges were laid. Instead, the NIS apparently sent the file to Milner, the Canadian commander in Kandahar.

"A major concern for the complainant appears to be his or her perception that the matter was deliberately ignored or even 'covered up,'" McCormack wrote.

"The complaint specifically alleges charges were 'ignored' and emphasizes there has still not been any court martial or charges to this day, despite the conduct of the [NIS] and subsequent investigations."

McCormack said that fact alone is a serious concern that might warrant its own investigation.

The NIS is supposed to exercise its investigative power outside the chain of command, not with deference to it, or even in consultation with it.

"This raises questions of [military police] independence on a systemic level," McCormack wrote. "Where the independence of the military police from the operational ... chain of command is put in issue, whether through allegations of interference or of an abrogation of responsibility."

Questions raised about commander

Milner is now a major-general and commander of the 1st Canadian Division. He's currently leading part of a large NATO exercise in Europe.

In an email to CBC News, Milner said he'd answer questions about the incident next week following his return to Canada.

Afghanistan Troops Return 20110722

An anonymous tip alleges Brig.-Gen. Dean Milner, who was a commander in Afghanistan, covered up mistreatment of Afghan detainees. (Canadian Press/Adrian Wyld)

There seems to be little doubt about the broad facts of the investigation.

The original complaint letter named five soldiers who were said to be witnesses to the events in Kandahar in January 2011. When the complaints commission investigators contacted those witnesses, they learned of two more troops said to have knowledge.

"The information received from these individuals confirmed that an incident did occur at the Detainee Transfer Facility in Kandahar in the time period alleged and raised several additional questions," McCormack wrote.

"The information obtained by the MPCC from some of the individuals contacted as references tends to indicate that there was a perception on the part of some of the members deployed to Kandahar Airfield at the time that some of the decisions made about the investigations and their ultimate outcome were made as a result of orders coming from 'Ottawa' and/or because of concerns about the reputation of the MP or CAF in light of the public attention issues involving the treatment of detainees can receive."

Alleged abuse amounts to a 'war crime' 

Human rights lawyer Paul Champ says the abuse amounts to a war crime under the Geneva Conventions, which makes the failure to lay charges even more troubling, especially considering the political context at the time the alleged abuse first occurred.

Paul Champ Ottawa labour lawyer Francisco Munoz hand sanitizer

Human rights lawyer Paul Champ says the alleged abuse would amount to a war crime under the Geneva Conventions. (CBC)

At the end of 2010 and the beginning of 2011, Champ was leading a case for Amnesty International at the Military Police Complaints Commission, during which he argued Canadians had committed war crimes by transferring Afghan detainees caught on the battlefield to Afghan prisons, where there was a significant risk of torture.

Military police were responsible for detainee handling, and also would have had the responsibility to investigate allegations of wrongdoing such as war crimes.

"At that time, the Canadian military police chain of command would have been very alive to the sensitivity of the handling of detainees, and moreover the Canadian Forces senior command would have been alive to the sensitivity of it, and yet it appears they carried out this completely shocking operation," Champ said in an interview.

"It appears that the perception of many soldiers on the ground was that there was interference with Ottawa into a proper investigation and accountability over this incident, and frankly that has echoes all the way back to the Somalia Inquiry in the 1990s."

In fact, it was the Somalia inquiry and allegations of a coverup there that led the Canadian Forces to create the National Investigation Service in the first place.

SOMALIA

Defence staff confer during a break in the inquiry into the deployment of Canadian Forces to Somalia, in October 1995. The inquiry, and allegations of a coverup, led the Canadian Forces to create the National Investigation Service. (Fred Chartrand/Canadian Press)

It was designed to be independent of the chain of command so that it could lay charges as its investigators saw fit without relying on the advice of commanders.

The Somalia Inquiry Report also led to the creation of the Military Police Complaints Commission itself.

"The allegations in this complaint, if validated, would raise issues about the [NIS] willingness or ability to investigate misconduct by or CAF members," the commission chair wrote.

The possibility that a lack of independence may exist — leading the [NIS] to make decisions about the laying of charges based on considerations unrelated to policing ... would go to the core of military policing and would raise questions about the ability of the [NIS] to perform its important role."

In a statement, the Defence Department said it welcomed the investigation.