The Conservative government's latitude to choose its own policies was curtailed yet again on Friday when a judge called health-care cuts for failed refugee claimants, and those from countries deemed by Ottawa to be safe, a form of "cruel and unusual treatment" and ruled them unconstitutional.

The ruling by Justice Anne Mactavish of the Federal Court in Ottawa was the latest sign that the executive branch of government and the judiciary are in open conflict.

So rare is the use of Section 12 of the Canadian Charter of Rights and Freedoms – "cruel and unusual treatment or punishment" – that neither the government nor the refugees' representatives were able to identify a single successful claim outside of criminal cases.

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"It's huge – it opens up a whole new claim that we can make when we want to challenge government conduct," Lorne Waldman, who represented the Canadian Association of Refugee Doctors in the case, said in an interview.

Justice Mactavish said the government's two-year-old policy of denying health care to certain classes of failed refugee claimants amounted to cruel and unusual treatment because it intentionally targeted vulnerable children and adults. She said it put at risk "the very lives of these innocent and vulnerable children in a manner that shocks the conscience and outrages our standards of decency." She gave the government four months to restore the health-care funding.

In widely different areas, the courts have barred the Conservative government from doing what it wished to do – close a Vancouver medical clinic at which drug users inject heroin under a nurse's supervision; turn the Senate into an elected body without provincial consent; appoint a Federal Court justice to one of three Quebec seats on the Supreme Court; limit prisoners' right to sue over the conditions of their detention; extend sentences for thousands of prisoners without being explicit about it; and change a parole law retroactively.

In this case, the government argued that it had the right to try to deter bogus claimants from coming to Canada, or overstaying, by denying them medical care, except where they had diseases that could spread to others. It said the cuts would save $80-million over four years, and those denied care could turn to charity, emergency rooms or private insurance.

Immigration Minister Chris Alexander said the government will appeal the ruling. "Failed claimants and those from safe countries like the U.S. or Europe should not be entitled to better health care than Canadians receive." (The government would need to seek a stay of Justice Mactavish's order if it wishes to continue with the cuts while an appeal is being heard.)

The refugee and medical advocacy groups that challenged the policy documented for Justice Mactavish 40 cases in which the denial of medical insurance created hardship. Hanif Ayubi, a rejected claimant from Afghanistan, was denied insulin and other medication for severe diabetes. As a dishwasher earning $10,000 a year, he could not afford private insurance. Daniel Rodriques, a failed claimant from Colombia, was denied an emergency operation after his retina detached. A doctor waived his fee and Mr. Rodriques had the operation shortly afterward.

Editor's note: An earlier version of this story said the cuts applied to failed refugee claimants. The cuts also apply to refugee claimants from countries the government deems safe.