Earlier this week, the department mailed 40,000 letters to medical marijuana users across the country, alerting them to major changes coming in the program beginning April 1.
But the letters arrived in an envelope that referred explicitly to the Medical Marijuana Access Program, with the name of the patient on the outside.
George Da Pont, deputy minister at Health Canada, issued an apology on the Health Canada website Thursday, calling the mailout an administrative error.
He says the department has been in discussions with the privacy commissioner about the incident.
"I have been advised that as the result of an administrative error the envelopes were labelled to indicate that they were sent by the program," said the apology. "This is not standard Health Canada practice."
"On behalf of Health Canada, I deeply regret this administrative error. Health Canada is taking steps to ensure this does not happen again."
Medical marijuana user Marcel Gignac says the gaffe has painted a target on the backs of medical marijuana patients across Canada, many of whom now fear home invasions.
"Patients are a little upset," Gignac said from Amherst. N.S. "Health Canada put thousands of the most vulnerable at risk."
Gignac, who is also spokesman for the Medicinal Cannabis Patients Alliance of Canada Inc., said the outing exposes patients socially as well as to thefts.
He said the department has previously used registered mail and discreet envelopes that do not spell out the medical marijuana program when communicating with patients.
A spokesman for Health Canada said no one was immediately available for comment.
The privacy commissioner's office said officials first learned of the problem through individuals who contacted them.
"Our office was not notified by Health Canada of this incident," said spokeswoman Heather Ormerod.
"We were made aware of it by a number of concerned individuals who contacted our office. We have since received complaints and we will be investigating this matter."
Health Canada is changing its medical marijuana program to allow dozens of approved commercial growers to provide the product to licensed patients, while phasing out personal production.
Some patients have said the move could increase prices dramatically for users with little or no income.