OTTAWA - A series of top-secret investigations into the conduct of Canada's elite commandos in Afghanistan is looking at not only the actions of soldiers in the field, but also of Ottawa-based commanders -- a fact that has alarmed military experts.

A spokesman for the Canadian Forces says an ongoing criminal investigation by military police and a separate, technical inquiry are examining how the chain of command responded to serious allegations levelled by a member of Joint Task Force 2 -- known as JTF-2.

Capt. Dave Scanlon said claims by the soldier were directed against another member of the highly trained special operations forces unit and there were "allegations against related actions (taken) by the SOFCOM chain of command."

He refused to get into details of the accusations and defended the blanket of secrecy that has covered the two criminal investigations, one of which is ongoing, and a board of inquiry.

"People characterize what has been going on as secret, or quiet, but police forces don't normally announce every investigation they undertake," Scanlon said Tuesday. "We're dealing with an organization that is in the counter-terrorism business."

A senior officer at National Defence headquarters tried late Tuesday to take some steam out of the controversy by asking for time to let justice take its course.

"Any speculation about these matters while investigative processes are ongoing is unhelpful and may taint the environment in which the investigation is taking place," said Rear Admiral Bob Davidson, of the Strategic Joint Staff, the nerve centre of the military.

"We cannot comment further on this matter. We ask that the independent investigation process be respected while it follows its course."

A military legal expert said the investigation immediately needs to be taken out of the hands of military police and placed with some other independent body.

"Holy cripes, how can the military be investigating itself here?" retired colonel Michel Drapeau said Tuesday.

He said if the allegations were as simple as the misconduct of an individual special forces soldier then the Canadian Forces National Investigative Service -- CFNIS -- is the perfect vehicle, but when there are claims that those giving the orders are somehow implicated then the only solution is an outside agency.

"When you're talking special operations you're talking about a very, very short chain of command that extends from the field to a one-star (general) to the (chief of defence staff) and who's going to investigate that?" said Drapeau.

One of the mandates of the independent CFNIS, which was created following the Somalia abuse scandal, is to investigate the chain of command, but Drapeau says no military body can be truly independent, especially when there is so much secrecy involved.

Scanlon acknowledged there is a "potential link" to the handling of Taliban prisoners, but the probes are separate from the ongoing, explosive controversy into potential torture by Afghans in Kandahar jails.

A soldier, who spent three years travelling in and out of Afghanistan on special forces operations, complained about the conduct of a colleague in June 2008, which sparked a military police investigation.

Scanlon said that probe concluded in October 2009 with no charges being laid. But about halfway through the investigation more allegations surfaced, which prompted a board of inquiry probe in February 2009 and then finally a second criminal investigation, which began in October 2009.

The military will not say what the soldier under investigation may have done wrong and also refused to discuss the scope of the inquiry.

There are "classified terms of reference," said Scanlon. "But what I can say is that the BOI is looking at allegations that are non-criminal or administrative in nature."

Boards of inquiry are conducted whenever the military believes its procedures or systems have failed and need improvement. The legal scope of those investigations has been made public in the past, most notably in the fatal submarine fire involving HMCS Chicoutimi.

Drapeau said the Canadian military's handling of the special forces investigation stands in stark contrast to the relative openness of the American probe of the conduct of its special forces in Afghanistan.

U.S. Army special forces soldiers were accused of botching a raid last February in Khataba, a village outside Gardez in eastern Afghanistan. The highly trained soldiers were accused of killing five people, including two pregnant women, and then trying to cover up the mistake, allegations that have been dealt with in public.

Liberal House leader David McGuinty expressed concern Tuesday and said there was more than meets the eye, particularly since it was a soldier who broke ranks to raise the alarm.

"It's particularly worrisome for me that this whole matter was broken apparently or revealed by a JTF-2 member," said McGuinty.

He said Defence Minister Peter MacKay has been asked repeatedly whether he knew of any ongoing investigations -- or additional torture allegations beyond what's already on the public record.

Meanwhile, a senior officer who helped direct the war in Afghanistan has defended the amount of information military police received about possible torture by Afghan intelligence officers.

Lt.-Gen. Andre Deschamps, now the air force chief, says the system of keeping everyone in the loop whenever a suspected Taliban fighter is captured evolved over time.

The Military Police Complaints Commission is investigating what military police knew -- or should have known -- about the alleged torture of prisoners after Canadians turned them over to Afghan authorities.

The commission has heard testimony suggesting military police were deliberately kept in the dark -- and perhaps even obstructed -- by the overseas headquarters based in Ottawa.

Deschamps was chief of staff for operations at the Canadian Expeditionary Force Command -- CEFCOM -- from 2006 to 2008 and says he doesn't believe military police had any responsibility for prisoners once they were out of Canadian custody.

He also said the Taliban routinely make up allegations of torture in order to keep the Canadians off balance.

He says CEFCOM had an officer specifically assigned to follow the prisoner file and information about conditions was funnelled toward that person and not deliberately kept out of the hands of MPs.