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Brigadier-General Guy Laroche speaks to reporters at Kandahar Air Field on Sept. 25, 2007, in Afghanistan.DENE MOORE/The Canadian Press

With all the blame-laying surrounding the detainee controversy, another less-scrutinized conflict may be at its core: the fractious relationship between the two Canadian bureaucracies entrusted with prosecuting the Afghan war.

On Tuesday, a former military commander's testimony at a probe into detainee handovers laid bare the peevish wrangling between the Department of Foreign Affairs and the Canadian military over who is to blame for lapses in prisoner monitoring.

The constant struggle for Canada in handing over battlefield captives to local interrogators is ensuring Afghanistan's torture-prone National Directorate of Security (NDS) doesn't abuse these prisoners. This requires frequent and thorough visits to Afghan jails.

But Brigadier-General Guy Laroche told the Military Police Complaints Commission Tuesday of troubling gaps in monitoring that occurred in the summer and fall of 2007 - months after the Harper government had boasted of upgrading protections for prisoners.

They were enough to warrant a complaint to his commander, Lieutenant-General Michel Gauthier, and give him pause about the safety of transferring prisoners.

"The situation was becoming critical due to the lack of visits in the various prisons," Brig.-Gen. Laroche told the complaints commission. "Because of that, I considered the light was amber."

The division of labour between the military and Foreign Affairs on detainees is that soldiers decide whether it's safe to transfer prisoners but it's diplomats who inspect jails for signs of torture.

Each side apparently harbours beefs about the job the other is doing.

Inspection visits dwindled to just a handful by September, 2007 - and zero for the month of October, Brig.-Gen. Laroche told the commission hearings.

"One thing is for sure, is that there were not enough visits," he said.

When the general put pressure on Foreign Affairs to step up its efforts, the response was to blame the military, the hearings heard. Foreign Affairs replied that it wasn't conducting more inspections because the military wasn't providing the resources to mount security convoys that could escort diplomats to prisons.

Brig.-Gen. Laroche on Tuesday called that "not credible."

After more lobbying on his part, inspection visits resumed in November, 2007 and immediately found a case of torture. This revelation caused the Canadian commander and his subordinate to halt transfers for three months - in part because they were worried about Canada's lack of monitoring.

He didn't budge easily when a seasoned diplomat pushed for transfers to resume following a raft of improvements. Brig.-Gen. Laroche rejected a January, 2008 effort by David Mulroney, Ottawa's lead bureaucrat on Afghanistan, to resume handovers. "My comments at the time were 'No, it's not good enough,' " he said.

Transfers resumed a month later under a new regime that included more frequent visits, more training for NDS officials on interrogation and video cameras in detention rooms.

The grumbling goes both ways. In March a senior Foreign Affairs official blamed the military for shortcomings in inspecting for torture, saying Forces brass have hindered this "monumental task" by refusing to help diplomats do it.

Cory Anderson criticized the military for failing to use close connections to Afghanistan's intelligence service to help diplomats with inspections.

Instead of using ties with the NDS to pry more information out of the intelligence agency, the Forces do little more than ferry diplomats to their inspections, Mr. Anderson told a Commons committee.

Mr. Anderson said this places "the monumental task of monitoring within an inherently secretive institution such as the NDS on a handful of Canadian civilians" who are "viewed with suspicion."