The former commander of Canadian soldiers in Afghanistan, Brig.-Gen. Daniel Menard, will face a court martial in relation to allegations he had an in-theatre intimate relationship with a member of his staff, the Department of National Defence announced Tuesday.

Allegations of a sexual affair first surfaced in May 2010 when Menard, a 26-year army veteran, was the Task Force Commander in Afghanistan.

The military police initiated an investigation after Menard's female subordinate, Master-Cpl. Bianka Langlois, said she had an affair with the married father of two. He was removed from his post in June and ordered home in disgrace.

In July, Menard was charged with two counts of prejudice of good order and discipline in relation to alleged inappropriate conduct under fraternization rules; and four counts of obstructing justice.

Military regulations prohibit soldiers, even married couples, from having intimate relations on deployment.

In its statement on Tuesday, the DND said the "Court Martial Administrator will convene the Court Martial at the first available date and at a location to be determined."

Langlois was also charged with a single charge of prejudice of good order and discipline in relation to the alleged inappropriate conduct, but there has been no announcement yet on whether the military intends to proceed with a court martial.

Brig-Gen. Jonathan Vance took over as commander of Task Force Kandahar after Menard was dismissed in May. The current commander is Brig.-Gen. Dean Milner, who took command from Vance at a handover ceremony at Kandahar Airfield in early September.

This is the second court martial that Menard has faced this year.

In March, Menard's assault rifle accidentally shot off two rounds as he was preparing to board a helicopter in Kandahar. No one was injured in the incident.

Menard handed over his weapon for inspection and it was found that there was no mechanical problem with the gun.

Menard admitted to troops that he was responsible and at his court martial, he pleaded guilty to one count of "neglect to the prejudice of good order and discipline" under the National Defence Act. He was also ordered to pay a $3,500 fine for his neglect.