The department says it will share relevant information — including the names and addresses of those who flout the new system — with law enforcement.
Under the existing federal program, thousands of people have licences to cultivate marijuana for personal use to help ease painful symptoms.
Beginning April 1, the government plans to allow only select commercial producers to grow marijuana under "secure and sanitary conditions" for postal distribution to medically approved patients.
Health Canada says anyone other than a licensed producer growing marijuana as of that date is breaking the law.
It means those who now possess or grow marijuana under the old rules must destroy and dispose of plants, seeds and dried pot by March 31. The Health Department recommends breaking up plant material, blending the marijuana with water, mixing it with cat litter to mask the pungent odour, and putting it all out with the trash.
It is sending letters to those enrolled under the old rules to say they must submit a signed form by April 30 confirming they have stopped growing pot. Users are also required to list the number of plants — and the number of grams of dried marijuana and seeds — they have destroyed.
Those who fail to comply will be reported to police, Health Canada says in a notice on its website.
The department will also "continue to co-operate with police, and provide information needed to protect public safety, as appropriate."
However, it will stop short of providing municipalities with a list of marijuana production sites that must shut down under the new rules, saying such information is protected by federal privacy law.
The federal threat to involve police amounts to criminalizing patients, said Legalize Canada, a group that plans to support federal electoral candidates who endorse legalization of marijuana.
The Conservative government recently floated the prospect of allowing police to ticket — instead of criminally charge — people for simple pot possession, the group noted.
"The hypocrisy is astounding."
On Tuesday, several British Columbia residents will ask the Federal Court of Canada for an injunction that would allow them to continue producing their own pot or have a specially designated person do so for them.
They argue the planned new system would deny them a safe, affordable supply of the particular strain of marijuana that meets their medical needs. They also contend that denying people the right to produce their own pot would violate their Charter of Rights guarantee of "security of the person."
The number of people authorized to possess — and often grow — marijuana under the federal program has risen to 37,000 this year from fewer than 100 in 2001.
In a court document defending changes to the program, the government says growing marijuana at home poses hazards including mould, fire, toxic chemicals and the threat of home invasion by criminals.
The government also rejects the constitutional argument, saying the charter does not guarantee the right to produce one's own medication.
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