Judge Anne Mactavish said in her decision that "detainees held by the Canadian forces in Afghanistan have rights accorded to them under the Afghan constitution and by international law, and, in particular, by international humanitarian law."
But, "they do not have rights under the Canadian Charter of Rights and Freedoms," she said.
The case was brought before the federal court by rights groups angered by allegations that Afghan prisoners transferred from Canadian to local custody were tortured.
Last month, the Canadian military said it had resumed the transfer of detainees in Afghanistan to local authorities, interrupted in November after it found "credible evidence" of prisoner abuse and following pressure from rights groups.
Lieutenant-Colonel Grant Dame said then in a televised address from Kandahar in southern Afghanistan, where Canadian forces are based, that detention facilities had been upgraded at a cost of 1.5 million dollars, Afghan jailers had undergone human rights training, and one senior Afghan official was fired and is now in custody.
An investigative report by the Toronto-based Globe and Mail last year uncovered "a litany of gruesome stories and a clear pattern of abuse by the Afghan authorities who work closely with Canadian troops."
The daily reported, based on interviews with 30 former prisoners of Kandahar jails, that the detainees suffered whips with electrical cables, electric shocks, exposure to cold temperatures and beatings.
There was no mention of abuse by Canadian forces.