In a statement issued late Wednesday, MacKay said he intends to inform the families of Williams' victims "of this terrible mistake" and offer his sincere apologies "on behalf of the entire military family."
Williams, once a rising star in the military and commander of Canadian Forces Base Trenton, was sentenced to life in prison in October 2010 after pleading guilty to the murders of Cpl. Marie-France Comeau and Jessica Lloyd.
He was also convicted of two sexual assaults and dozens of fetish break-ins.
The Canadian Forces stripped him of his rank after his conviction and, in a rare move, burned his uniform.
MacKay said as soon as he became aware of the photo, he immediately ordered the military to destroy all copies of the collected booklets.
"I have also instructed my officials to immediately begin an investigation to ensure it does not happen again,' said MacKay.
"This is a terrible mistake for which the Canadian Forces are truly sorry."