The Canadian military has ordered a formal investigation into the beating of an Afghan prisoner. (Canadian Press)

The Canadian military has ordered a formal investigation into how a critical report on the beating of an Afghan prisoner remained buried at National Defence headquarters.

In June 2006 soldiers captured a suspected Taliban fighter and handed him over to local police, who then beat him to the point where the Canadians had to intervene.

A report on the incident, which undermines Conservative government claims that no prisoners handed over to Afghans faced abuse, was apparently uncovered only in December.

Chief of Defence Staff Gen. Walt Natynczyk ordered an investigation, which is headed by Rear Admiral Paul Maddison, commander of Joint Task Force Atlantic.

Natynczyk's deputy, Vice-Admiral Denis Rouleau, said the probe will look at the incident itself, why soldiers took the actions they did and how it was reported. The report of the investigation is due March 1 and is to be made public shortly after.

Diplomat Richard Colvin testified before a special House of Commons committee in November that he repeatedly warned federal officials in 2006 and 2007 that prisoners faced the possibility of torture in Afghan jails. His warnings were dismissed by the government and the military as vague and unsubstantiated.

The June 2006 incident was made public almost two years ago, but the military initially disputed the version of events, saying its soldiers never captured the prisoner in the first place.

Natynczyk's admission that Canadians had indeed been the ones to detain the suspect caused shock waves on Parliament Hill and prompted accusations of a coverup.