An Afghan agency, at one time entrusted to monitor Canadian-captured insurgents in Kandahar, says it has documented nearly 400 cases of torture across the war-ravaged country.
The latest report from the Afghanistan Independent Human Rights Commission, a translated version of which was obtained by The Canadian Press, comes as Canada's top military commander confirmed the army halted transferring prisoners to Afghan authorities on more than one occasion.
Speaking at the close of an international security conference in Halifax, General Walter Natynczyk wouldn't say how many times the transfers were stopped.
There has been only one occasion when the federal government has publicly acknowledged that the army stopped handing over prisoners - in November, 2007 - because of torture concerns.
The general said he couldn't offer details because he didn't want to pre-empt statements that former military commanders are expected to make before a special House of Commons committee this week.
The human-rights report and Gen. Natynczyk's comments were made amid a continuing political firestorm created by former diplomat Richard Colvin, who last week dropped a bombshell when he alleged that all Canadian-captured prisoners were abused early in the mission.
The Conservative government has described Mr. Colvin's allegation as hearsay, unsubstantiated and "simply not credible."
However, the Afghan commission said it uncovered 47 cases of abuse in Kandahar, which was ranked third in terms of the number of abuse claims in the country.
"Torture and other cruel, inhuman or degrading treatment are common in the majority of law enforcement institutions, and at least 98.5 per cent of interviewed victims have been tortured," said the commission's April, 2009, study.
The independent study, which tracked abuse claims between 2001 and early 2008, shows the vast majority of them - 243 - were levelled in 2006 and 2007.
That is the time frame when Mr. Colvin was in Afghanistan and warning the federal government about torture.
The human rights commission, which is funded and mentored by Canada, signed a formal agreement with Ottawa in February, 2007, to monitor prisoners captured by Canadian soldiers.
The deal was scrapped when the Conservative government rewrote its transfer arrangement with the Afghan government a few months later and began its own regular prison visits.
It is unclear whether Canadian diplomats have ever examined the evidence uncovered by the commission - either in the latest controversy or when allegations of abuse by Afghans first became public in spring 2007.
Defence Minister Peter MacKay, who has led the charge to discredit Colvin's allegations, said he doesn't know whether the Foreign Affairs Department has looked at the prisoner interviews.
"I couldn't comment on a veracity or the evidence that's found within the pages of those reports," MacKay said.
"What I can tell you is, what has been placed before a Parliamentary committee thus far is simply not credible. There is not a single, proven allegation."
A former European Union diplomat is mystified at Ottawa's insistence that there is no "first-hand" evidence of torture.
"Taking a stand against torture is fundamental to what Canada is doing there and certainly we in the European Union are doing," said Michael Semple, a Harvard Carr Center expert who spent years in Afghanistan.
"We just want to make sure all of us are on the right side of this debate. We are against torture. We take a stand against torture. We'll do everything we can to stop it. We haven't managed to stamp it out yet. We know that torture is ongoing and we're prepared to do more to stop it."
Mr. Semple, an Irish diplomat who ran afoul of the Afghan government for independently trying to draw the Taliban into peace talks, was a speaker at the weekend security conference.
The human rights commission report said 14 per cent of the torture cases involved Afghanistan's notorious intelligence service, the National Directorate of Security.
NATO forces, including Canada, usually hand over their prisoners to the NDS.
British forces halted prisoner transfers last summer because of abuse concerns. It's unclear whether they have resumed.
Mr. Semple said the unfolding controversy in Canada should be used to confront the Afghan intelligence agency.
"Simply taking promises that it won't happen aren't good enough," he said.
Mr. Semple said Canada, the United States and other allies should march into the NDS in Kabul, threaten to stop paying the bills and say: "We can't back institutions that are involved in torture."
The human rights report said that iron rods, electric shocks and beatings constituted the preferred methods of torture and most often it was done to extract a confession.
The top Afghan provinces for torture were Kapisa, northeast of Kabul, and Herat in the western part of the country.
The vast majority of the abuse was carried out by Afghan police officers, according to the report.
NDP foreign affairs critic Paul Dewar said there is a mountain of evidence in reports from other agencies, including the U.S. government.
"It's Minister MacKay's word against the facts reported by the AIHRC, Amnesty International and even the U.S. State Department," he said.
Follow us on Twitter: