CBC News says the elaborate theft of Canadian Forces materiel was discovered when the shipping containers were opened in Montreal.
The Department of National Defence is confirming that various military hardware and gear is missing while insisting that none of the breached containers were carrying weapons, munitions or uniforms.
A full investigation into the theft is underway.
Montreal company A.J. Maritime is responsible for shipping goods back to Canada following the shutdown of the Canadian base in Kandahar last November.
The company's president, Alda Rodrigues, told the CBC program Power and Politics that pilfering has been a widespread problem in the shipping operations.
"The situation in Afghanistan and Pakistan is volatile. Pilfering is occurring. But Canada is not alone," she said.
"All NATO countries have a pilfering problem with their containers. No one knows where the pilfering is occurring."
The situation is further complicated by blockades of NATO supply crossings at the Afghan-Pakistan border. A.J. Maritime says there are still 448 Canadian shipping containers in Afghanistan. About 40 are currently in transit via a port in Pakistan.
The number of containers that were compromised is unclear, as are details about exactly what equipment is missing. The resulting costs are also unknown. The Department of National Defence says that only low-priority equipment is shipped through Pakistan.