He said Lieutenant General Marc Lessard, commander of Canadian forces abroad, had relieved Menard of his command because of an "alleged inappropriate personal relationship".
Menard has been on leave from Afghanistan for several weeks. On Tuesday, he pleaded guilty at a court-martial in Canada to accidentally firing his weapon at Kandahar Air Field in March and was fined.
Brigadier General Jon Vance will temporarily assume command of Canadian forces in Afghanistan, a job he held previously, the military said. He will be replaced by Brigadier General Dean Milner.
"There will not be a significant delay" in the leadership change, Hetherington said.