Canadian soldiers conduct a patrol in southern Afghanistan in June 2009. Canada's Defence Department has been probing the actions of the military's elite special forces unit in Afghanistan, CBC News has learned. (Colin Perkel/Canadian Press)

Canada's Defence Department quietly began a major inquiry into the Afghanistan operations of the military's elite special forces unit two years ago, CBC News has learned.

The investigation began in 2008 after a member of the highly secretive task force, known as Joint Task Force 2 or JTF2, raised serious allegations against another member of the force and the force in general, the military has confirmed.

The allegations centred on events that took place between 2005 and 2008, said navy Capt. David Scanlon, but he would provide no details about them.

Military briefing note Read the 2009 note on Sand Trap written by Gen. Walter Natynczyk, Canada's chief of defence staff.

The investigation, called Sand Trap I, ended after a few months with no charges laid, but the probe sparked a larger investigation into broader allegations. That investigation, called Sand Trap II, is still underway.

CBC News has learned the handling of detainees may have triggered the initial investigation, although the current probe is much wider than that.

The Sand Trap investigations should not taint the reputation of the military, Scanlon said.

"The Canadian Forces have been operating in the very complex Afghan theatre for almost a decade, and the vast majority of Canadian Forces personnel are performing their tough assignments with typical Canadian honesty and integrity," he said.

Briefing note to MacKay

A few details of the investigation are contained in a November 2009 military briefing note written by Gen. Walter Natynczyk, Canada's chief of defence staff, and obtained by the CBC through an Access to Information Act request.

In the note, Natynczyk tells Defence Minister Peter MacKay that a board of inquiry is investigating Sand Trap II and started hearing from witnesses in May 2009. Military boards of inquiry are called to formally investigate accidents, misconduct or other major problems within the Canadian Forces.

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At the time the note was written, Natynczyk wrote that 60 witnesses had testified before the board, and another 40 still needed to give testimony. He expected testimony to be complete by December 2009, with a report submitted by April 2010.

Scanlon said the board of inquiry is focusing on the broader administrative and non-criminal aspects of the allegations at the heart of Sand Trap II.

He said investigators are receiving full co-operation from the special forces unit, and any charges that might arise would be be made public.

High-risk operations

The military has never said much about the work of JTF2, although it has revealed the unit has been involved in high-risk operations against high-value targets, including Taliban and al-Qaeda commanders.

The unit has also been involved in pursuing insurgents who build and plant roadside bombs, and the networks that supply them, the military has said.

During the three year period at the centre of the Sand Trap investigations, 2005 to 2008, the JTF2 unit was attached to an American special forces command based in Kandahar. JTF2 took its tactical direction from the Americans.

The Sand Trap investigations are not part of the Military Police Complaints Commission (MPCC) public hearings into allegations that military police failed to investigate senior officers responsible for transfers allegedly involving a risk of torture.

"This is a distinct and broader investigation," Scalon said. "Far broader than anything the MPCC would look at."