The former commander of Canadian soldiers in Afghanistan, along with a female subordinate, have been charged by the Canadian Forces Military Police for offences related to a sexual affair in-theatre.

The military police initiated an investigation after Master-Cpl. Bianka Langlois said she had an affair with Brig.-Gen. Daniel Menard.

Menard was charged with two counts of prejudice of good order and discipline in relation to alleged inappropriate conduct under fraternization rules.

He is also facing an obstruction of justice charge and a separate count of conduct to the prejudice of good order and discipline.

Langlois faces a single charge of prejudice of good order and discipline in relation to the alleged inappropriate conduct.

Meanwhile, Canada's most senior officer in Haiti was relieved of command last month and faces a number of allegations, including of having an inappropriate relationship.

Military police are investigating Col. Bernard Ouellette, who was also chief of staff to the UN mission in Haiti.

The military says the allegation of an inappropriate relationship did not involve another member of the Canadian Forces. And CTV News has learned that Ouellette had allegedly been having an affair with a female United Nations worker, according to military sources.

Military law disallows soldiers, even if they are married, from having intimate relations while deployed.

Menard was relieved of his Afghanistan command after the allegations came to light in May and was assigned to a staff job in Ottawa instead of returning to be head of the army in Quebec as planned.

Instead, Brig.-Gen. Alain Tremblay, was assigned to the Quebec posting.

The military has faced a number of high-profiles charges against top level officers in recent months.

In one shocking case, Col. Russell Williams, the former commander at CFB Trenton, the country's biggest air base, was arrested and charged with two counts of murder and sex-assault related charges.

With files from The Canadian Press