Foreign Affairs Minister Maxime Bernier made the revelation in the House of Commons while answering a question from a Conservative member, saying the prisoner was being held in "conditions that concerned" Canadian officials.
If verified, it brings to seven the number of complaints Canadian authorities have received since Ottawa signed a revised prisoner transfer agreement with the government of Afghan President Hamid Karzai.
Published reports last spring said as many as three dozen prisoners —captured by Canadian troops, but handed over to local authorities — complained of being beaten and abused prior to the signing of a new transfer arrangement last May. Six more cases surfaced in the wake of the new deal.
"The allegation has come to light, Mr. Speaker, because we have a good agreement with the Afghan government," Bernier told the Commons on Wednesday.
The new arrangement allows Canada the right to check on the prisoners it has captured — something it wasn't able to do up until last spring.
Both the Canadian and Afghan governments promised investigations into the allegations last spring, but no results have been made public.
Bernier said Canadian authorities have visited Afghan prisons, including ones operated by that country's notorious intelligence service, 32 times in the last five months.
Karzai's government announced Wednesday that it will look into overall complaints by Amnesty International that systemic torture is taking place in jails throughout the war-torn country.
The human-rights group said Monday that it "remains gravely concerned that detainees handed over by [NATO] to the Afghan authorities are currently at substantial risk of torture and other ill-treatment."
In a special report, Amnesty specifically criticized Canada's transfer agreement, describing it as flawed because the arrangement doesn't prevent possible torture, it only detects it afterwards.
Canada and other NATO countries, including Britain, the Netherlands, Belgium and Norway, should stop handing over captured fighters to local Afghan authorities, the group demanded.
Amnesty has been fighting a protracted legal battle in Federal Court, trying to stop Canadian prisoner transfers. The Foreign Affairs Department was set late Wednesday night to release thousands of pages of documents previously deemed secret that relate to the case.
Responding to Amnesty's renewed criticism, NATO spokesman James Appathurai said the military alliance was convinced that there was no systemic torture taking place in Afghan jails.
But a German general said Wednesday that NATO has heard of isolated, individual cases where prisoners have been tortured when they were handed over to local jailers.
"We are aware of individual cases where employees in Afghan prisons committed actions that, according to international law, certainly do not meet our expectations," Gen. Egon Ramms, a senior officer at the alliance's field headquarters in Kabul, told German media in an interview.
Bloc Québécois Leader Gilles Duceppe, who pushed the issue in question period, said Bernier obviously doesn't know what he is talking about and if authorities have uncovered a potential case of abuse, Canada is in trouble in the eyes of international law.
"If he's talking about one case, that is already in violation of the Geneva convention," Duceppe said. "Maybe he doesn't realize that. I think he doesn't even know what is the Geneva convention."
Canada has promised to treat Taliban prisoners with the same rights and dignity accorded under the Third Geneva Convention, but since their status is somewhat murky, it is supposed to hold battlefield hearings to determine whether the person they've captured is a bona fide insurgent. Those hearings have never happened, and the prisoners are simply handed over top Afghan authorities to sort out.
Amnesty argues that many of the detentions are arbitrary and the NATO dragnet sweeps up innocent civilians.
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