The Conservative government was aware of concerns about the state of prisons in Afghanistan in early 2006, prompting it to negotiate a new prisoner transfer agreement, Defence Minister Peter MacKay said Friday.

A 2005 agreement covering the handover of prisoners captured by Canadian troops to Afghan authorities was eventually renegotiated in May 2007 following media reports about torture in Afghan prisons.

MacKay's comments came a day after David Mulroney, Canada's current ambassador to China who headed the Privy Council's Afghanistan task force, told a Commons committee that Canadian officials were aware of allegations of mistreatment of prisoners and that "there was no doubt in anyone's mind that the Afghan system was riddled with problems."

However, Mulroney said there was no evidence that detainees being handed over by Canadian soldiers to Afghan officials were being tortured.

"Obviously there were concerns about the state of prisons," MacKay said outside the Commons. "There were concerns about allegations. There were concerns about information found in reports. There were concerns.

"The decision to change the transfer arrangement would have been as a result of a lot of sources of information including those from Mr. Mulroney, those from other individuals on the ground … those who went to Afghan prisons to observe the situation," MacKay said. "We acted on those concerns over two and a half years ago."

While the government had previously stated that a specific abuse allegation in the spring of 2007 prompted it to act, MacKay now suggests it was an evolution in thinking.

"I can't say that there was a specific moment in time that the decision to change the transfer arrangement crystallized in my mind," he said. "It was obviously made as a result of recommendations from within the department."

MacKay admitted that his office did receive two emails from diplomat Richard Colvin in May and June 2006 containing warnings from the International Committee of the Red Cross of prisoner abuse, but insisted again that he never saw them.

"All ministers receive thousands and thousands of emails," he said. "They are then vetted by officials within departments and officials within political staff. So if you're asking me if I saw two specific emails with Mr. Colvin's name attached — no."

Last week, Colvin was accused by Conservative MPs of being a Taliban "dupe" for believing and broadcasting claims of prisoner abuse — and testifying he'd relayed those concerns to an unreceptive government.

Former chief of defence staff Rick Hillier, retired general Michel Gauthier and Maj.-Gen. David Fraser appeared before the same Commons committee this week and emphatically refuted Colvin's testimony.

Hillier said Colvin's reports, which he subsequently reviewed, "said nothing about abuse, nothing about torture or anything else that would have caught my attention or indeed the attention of others."

With files from The Canadian Press