Media reports say more than C$10 million ($9.1 million) in gold and other assets are missing. Ottawa acted after it learned that an independent audit of the mint was not going to be able to solve the mystery.
"I have instructed the mint to call in the Royal Canadian Mounted Police to (do) a full investigation," junior government minister Rob Merrifield told reporters, declining to say how much was missing.
Opposition politicians said the incident showed the minority Conservative government was hopelessly incompetent.
"If they can't even hold on to the gold in the mint, what are they capable of doing?" asked New Democrat legislator Thomas Mulcair.
The mint says its plant in Winnipeg, Manitoba, produces over one billion circulation coins each year. It also says its vaults are "an exceptionally secure facility."