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Three detainees are escorted of a U.S. plane by Canadian special-forces troops as they arrive at Kandahar airfield in southern Afghanistan on Jan. 21, 2002.DARIO LOPEZ-MILLS/The Associated Press

A complaint from a soldier inside JTF2 - Canada's elite special forces unit - was the trigger behind a series of secret military probes into the handling of Afghan prisoners that only came to light this week.

The investigations have probed the alleged improper killing of Afghans, sources say.

The accusation of misconduct levelled by one member of Joint Task Force 2 against another came from an unusually tight knit group that considers itself a descendant of such units as the famed Devil's Brigade commandos of the Second World War.

Retired colonel Michel Drapeau, an expert in military law, said it would be tremendously daunting for a JTF2 soldier to break ranks from such an elite unit and launch a complaint.

"The missions on which they are deployed [are]unseen, unheard and unsupervised in many respects," Mr. Drapeau said. "It's a brotherhood, the bonds of which are unparalleled any place else for somebody to make allegations."

The Canadian Forces refuses to divulge details of the complaint - which concerns both a JTF2 soldier and the special forces chain of command, except to say it covered operations in Afghanistan between 2005 and 2008.

"The vast majority of Canadian Forces personnel are performing their tough assignments with typical Canadian honesty and integrity," Forces Captain Dave Scanlon said.

The normally secretive JTF2 has been waging a separate war in Afghanistan from the rest of Canadian Forces. Bound by somewhat different rules of engagement, they've been fighting in the shadows alongside the elite U.S. Special Forces, hunting down Taliban and al-Qaeda leaders.

The complaint led to three separate investigations within the Canadian military, Ottawa says. Two have yet to report.

The first, codenamed Sand Trap I, looked at the allegations against the JTF soldier and Canadian Special Operations Forces Command, which reports directly to the chief of the Defence Staff. Between 2005 and 2008 this was General Rick Hillier.

It spanned 16 months and reported in October, 2009. Forces officials say there was not enough evidence gathered to support laying charges.

But the military says it uncovered "additional allegations" during this first probe that triggered a second investigation, called Sand Trap II, which began in October, 2009, and has yet to conclude.

The Forces in 2008 also set up a board of inquiry into the matter that continues to this day.

Scott Taylor, editor of Esprit de Corps magazine, says boards of inquiry are an effective way for the Canadian Forces to clamp down on internal talk about the investigations.

"It's almost the internal effect of a gag order. It's to prevent people from going out to the media or saying anything," Mr. Taylor said.

He was reluctant to speculate what the substance of the JTF2 complaint was but said it could stem from a soldier's disquiet with how joint operations with the U.S. were conducted.

"It could be someone queasy about American procedures as opposed to our own," Mr. Taylor said.

"They [the Americans]do snatch-and-grab operations and this is what it could be."

U.S. special forces came under fire for a botched nighttime raid in eastern Afghanistan last February. NATO was forced to apologize after the soldiers were accused of killing five people including two pregnant women.

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