Canadian soldiers serving in Afghanistan have been ordered by commanding officers "to ignore" incidents of sexual assault among the civilian population, says a military chaplain who counsels troops returning home with post-traumatic stress disorder.

The chaplain, Jean Johns, says she recently counselled a Canadian soldier who said he witnessed a boy being raped by an Afghan soldier, then wrote a report on the allegation for her brigade chaplain.

In her March report, which she says should have been advanced "up the chain of command," Johns says the corporal told her that Canadian troops have been ordered by commanding officers "to ignore" incidents of sexual assault. Johns hasn't received a reply to the report.

While several Canadian Forces chaplains say other soldiers have made similar claims, Department of National Defence lawyers have argued Canada isn't obliged to investigate because none of the soldiers has made a formal complaint, says a senior Canadian officer familiar with the matter.

"It's ridiculous," the officer says. "We have an ethical and moral responsibility to pursue this, not to shut our eyes to it because it would make it more difficult to work with the Afghan government.

"We're supposed to be in Afghanistan to help people who are being victimized."

The independent claims bolster the credibility of an account provided by Cpl. Travis Schouten, a Canadian soldier who served in Afghanistan from September 2006 through early 2007 and now suffers from severe post-traumatic stress disorder.

A Star story Saturday detailed an allegation levelled by Schouten that during his tour, he heard an Afghan national army soldier abusing a young boy and then saw the boy afterwards with visible signs of rape trauma, his bowels and lower intestines falling out of his body.

The alleged abuse occurred in late 2006 near a forward operation base, some 20 kilometres from the Kandahar Airfield. Another chaplain at CFB Petawawa, Joe Johns, said a third chaplain told a group meeting last summer about having been approached by several Canadian military police officers who asked for help reconciling the fact they hadn't done anything to stop abuses. That chaplain declined to comment.

Bryon Wilfert, the Liberal critic for national defence, says he has asked party officials for approval to grill Foreign Affairs Minister David Emerson about the sex-abuse allegations today during Question Period.

Wilfert called Schouten's claims "very serious and disturbing" and says Canada at least should have sent the Afghan government a diplomatic note about the allegations. "Anybody who says this is about cultural differences should have their head examined," he says.

Maj. Paul Doucette, a Canadian Forces spokesperson, says the military is aware only of Schouten's allegation and intends to investigate. Doucette didn't say why an investigation hasn't already taken place. Schouten last month described the assault while testifying to the parliamentary subcommittee on national defence.

The testimony was given behind closed doors during a meeting in camera.

Doucette said in an emailed statement that "specific additional information would be required before any such issue could be raised with Afghan officials. However, allegations of this type of behaviour would be an issue for Afghan authorities to address under Afghan law."

Asked if Canadian Forces personnel are prevented from intervening in cases of abuse because of rules of engagement, Doucette wrote, "the general purpose of ROEs is to control the use of force by military forces in conducting their operations.

"All Canadian Forces members, whatever their rank and trade, are trained to inform their chain of command of significant incidents, especially when an incident clearly calls for decisions beyond their level of authority."

Lt. Col. Stéphane Grenier says he has spoken to Schouten, believes his story, and adds he has talked to another Canadian soldier who claims to have witnessed a similar assault. Grenier has also counselled a British soldier who said he watched a young boy being raped by an Afghan soldier while his senior officer concluded a meeting nearby with Afghan army officers.

The sexual-abuse allegations put Canada in a thorny position with the local Afghan government and rekindle memories of some past deployments that led to Canadian soldiers developing post-traumatic stress disorder (PTSD).

After serving in Bosnia, some soldiers were diagnosed with PTSD after rules of engagement prevented them from interfering when they witnessed civilians being raped by soldiers. Retired general Roméo Dallaire famously struggled with PTSD after the United Nations thwarted his efforts to stop a genocide in Rwanda in 1994.