The Harper government is under fire from critics who accuse it of being inept or misleading when it comes to the issue of the transfer of prisoners by Canadian soldiers in Afghanistan.

A federal court heard on Thursday that Canadian troops had halted the transfer of detainees to Afghan authorities in early November, one day after finding evidence of torture in an Afghan prison.

That came as a complete surprise to Canadians, human rights advocates, and politicians. Back in November, Maxime Bernier had said Canadian officials were concerned about a Taliban prisoner who alleged that he was tortured, but the foreign affairs minister did not mention that Canada had already halted prisoner transfers.

On Thursday, a federal official said that's because a Canadian colonel in Afghanistan made the decision and no one in the military told the government. Critics say that's hard to believe.

"I think there's been a complete lack of candour (by the Tories)," Bob Rae, the foreign affairs critic for the Liberals, told CTV Newsnet's Mike Duffy Live.

"The government knew what the decisions were on the ground. They must have been informed about them."

Critics say it's especially difficult to believe that the military would not have told the government about the change in policy because the issue of prisoner transfers was at the centre of a political firestorm at the time.

As late as the end of October, the Conservative government had questioned and even denied news reports that some prisoners captured by Canadians and turned over to the Afghans were abused. They suggested that the reports were unsubstantiated and part of Taliban propaganda.

But the opposition had hammered away at the issue in the press and in Parliament, and on Nov. 5, Bernier acknowledged that Canadians saw a Taliban prisoner with conditions that "concerned them."

On Nov. 6, the military stopped turning over prisoners to the Afghans and on November 14, Bernier admitted that torture allegations were in fact made. Critics now want to know why Bernier did not mention that prisoner transfers had by then already been halted for more than a week.

In a statement released Thursday, the Prime Minister's Office called the number of detainees and transfer of prisoners "operational matters."

"The government will not provide any comment on operational matters," said a PMO statement released Thursday.

Rae noted, however, the issue is far from an operational matter.

"The idea that you can brush this aside as some kind of an operational decision is frankly ludicrous. A decision as to what you do with prisoners is not an operational decision made on a day-to-day basis. It's a decision that's made as a matter of policy," he said.

Dawn Black, the NDP's defence critic, told Mike Duffy Live that she finds it difficult to believe that the military would not have informed the government about the change in policy.

"We live in a democracy where the government guides the policies of the Canadian Forces. It's not supposed to work the other way around," she said.

Responding to criticism by Rae and Black, Laurie Hawn, the parliamentary secretary to the defence minister, reiterated the PMO stance that the government does not "meddle, day-to-day, in the kinds of decisions (the military) is forced to make in a very tough situation, in a very tough part of the world."

When asked where detainees are being held now that Canada is no longer transferring them to the Afghans, Hawn said it was an "operational decision" of the military.

In court on Thursday, human rights groups sought a ban on transfers. But a federal lawyer argued it was a moot point because the transfers have been stopped. The government's lawyer was cut off by Federal Court Justice Anne Mactavish.

"Up until noon on Tuesday we thought there was a live controversy," she said.