The demand comes in the wake of a blistering United Nations report that documents the torture of suspected Taliban fighters in Afghan jails.
An Amnesty letter to Defence Minister Peter MacKay, obtained by The Canadian Press, warned that Ottawa's obligations under international law have not ceased just because troops are no longer capturing insurgents in the field.
The Canadian army handed over its portion of the battlefield in Kandahar in July as part of a withdrawal ordered by Parliament. It now runs a training mission in Kabul.
However, operations went on right up until the changeover and Canadian soldiers continued to turn prisoners over to local authorities, including the notorious National Directorate of Security, the Afghan intelligence agency named in the UN report.
"Given the widespread nature of these reports, it is likely that some of the prisoners alleging abuse were transferred by the Canadian Forces," wrote Paul Champ, the lawyer for the human rights group.
"Canada must immediately take action to confirm the physical condition of every individual transferred by the Canadian Forces to Afghan authorities."
The report does suggest, however, that Canadian-captured prisoners may have been treated better than those taken by other countries, perhaps due to pressure applied to Afghan authorities in the wake of a hot political debate in Canada over torture claims.
It quoted one prisoner as saying: "Except those arrested by Canadians, every single person arrested by NDS officials has to go through the similar experience I went through. Even the detainees handed over by Americans are interrogated by NDS and tortured.
"For those arrested by Canadians, two NDS officials were allocated for further interrogation and those interrogated by them never complained about ill-treatment by NDS officials."
It is unclear how many Canadian-captured fighters remain in the Afghan justice system. At the conclusion of the military and civilian missions in Kandahar, the Foreign Affairs left a staff officer to monitor those cases until the end of this year.
The letter to MacKay urged the Harper government to clarify its legal responsibility towards the prisoners that remain in the Afghan system and to press the Karzai government to take the torture allegations seriously.
"Canada must ensure that independent and competent investigations of these allegations are carried out, with charges and prosecution where appropriate. Unfortunately, there is no evidence that Afghanistan has properly investigated past allegations of abuse."
A complaint from Amnesty and the B.C. Civil Liberties Association started a public inquiry by the Military Police Complaints Commission into the transfer of suspected insurgents by Canadian soldiers.
The watchdog agency has yet to finalize its report into the question of whether military police knew, or should have known, about alleged torture.
Handing over prisoners to torture is a violation of international law.
The UN report, released Monday, painted a stark, alarming picture of systemic torture within the Afghan justice system. It fingered the country's brutal and corrupt police force as well as the intelligence service.
The report found evidence of a compelling pattern and practice of torture and ill-treatment among those detained by the intelligence service.
UN researchers found that Afghan police were somewhat less brutal and not as routine in their practise of abuse.
Use of interrogation methods, including suspension, beatings, electric shock, stress positions and threatened sexual assault is unacceptable by any standard of international human rights law, the report said.
Throughout the public hearings by the complaints commission, Canadian officials insisted there was no solid evidence of abuse. Although Canadian transfers were suspended on several occasions, they were never stopped entirely throughout the five-year combat mission in Kandahar.
When a draft version of the UN report was circulated a number of weeks ago, NATO stopped the handover of prisoners.
The Canadian government initially refused to monitor the prisoners turned over by the army, but it eventually set up such a system in the spring of 2007 after published reports revealed over two dozen suspected cases of abuse.
Champ said the level of diligence by Canadians has never been adequate. The British army mandates multiple follow-up visits to each prisoner it captures.
Brig-Gen. Tim Grant, a former Canadian task force commander, recommended in 2007 that Ottawa adopt a similar practice, conducting perhaps as many as three visits to each prisoner. Champ said that advice was ignored.
"Unfortunately, Brig-Gen Grant's advice on the appropriate level of monitoring was not followed and it was decided in Ottawa that even a single visit to every detainee was unnecessary," he wrote.
"In 2010, the England High Court of Justice ordered the British military to continue its rigorous monitoring regime, holding that regular, private interviews with each detainee were necessary to meet the minimum requirements under international human rights law. At a bare minimum, Canada should meet this same standard."