It is the latest salvo in a series of legal actions over how the government administers its medical pot program.
Earlier this month, Federal Court Judge Michael Manson ruled that patients currently licensed to grow their own marijuana would be permitted to produce the drug even after new regulations banning the practice take effect Tuesday.
The judge granted an application from medical marijuana patients seeking a temporary injunction to preserve the status quo until their constitutional challenge of the new system could be heard.
The government said Monday it will ask the Federal Court of Appeal to overturn the injunction.
Under the existing federal program, thousands of people have licences to cultivate marijuana for personal use to help ease painful symptoms of conditions such as diabetes and multiple sclerosis.
The government says growing marijuana at home poses hazards including mould, fire, toxic chemicals and the threat of home invasion by criminals.
It plans to allow only select commercial producers to grow marijuana under "secure and sanitary conditions" for distribution through the mail, in dried form, to medically approved patients.
Health Minister Rona Ambrose made it clear in a statement Monday that the only reason her department administers a program is a 14-year-old court ruling that said there must be reasonable access to a legal source of marijuana for medical purposes.
"I want to emphasize that marijuana is not an approved drug or medicine in Canada," Ambrose said.
However, the injunction stands for the moment, meaning patients can continue to grow pot — at least until the next ruling.
It is unclear when the federal appeal of the injunction will be heard.
If the government ultimately fails to overturn Manson's decision, it will leave the path clear for the patients' constitutional challenge of the planned new system.
As a result, the matter could be tied up in the courts for many months to come.
The number of people authorized to possess — and frequently grow — marijuana under the old federal program climbed to 37,000 this year from fewer than 100 in 2001.
Several patients permitted to cultivate their own pot — or serve as a designated grower for someone else — argue the planned new system denies ill Canadians a safe, affordable supply of medical marijuana.
Some say they can grow at home for pennies a gram, while official suppliers licensed by Health Canada charge anywhere from a discounted price of $3 a gram to as much as $13.50.
Denying people the right to produce their own pot would violate their Charter of Rights guarantee of "security of the person," the patients say.
The government rejects the constitutional argument, saying the charter does not ensure the right to produce one's own medication.
Ambrose said she continues to hear concerns from health professional organizations about prescribing marijuana.
Health Canada's statement also said Ambrose has been working with the department in recent months to address concerns about marijuana as a treatment, including the lack of dosage guidelines and appropriate health cautions.
Ambrose has also asked her officials to produce a document on marijuana for medical purposes — in consultation with the medical and scientific community — to help doctors and nurses make decisions, the department said.
"We expect these new measures, including information on dosage guidelines, educational material and increased oversight, will decrease the potential for over-prescribing and negative health impacts."
Several opponents of the planned federal changes — including lead counsel John Conroy — plan to talk about the case in Ottawa on Tuesday and hold a rally on Parliament Hill.
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