"Although we are disappointed with the Supreme Court of Canada's decision today, we will comply," she told the House of Commons.
"We believe that the system should be focused on preventing people from becoming drug addicts. A key pillar of the national, anti-drug strategy is prevention and treatment for those with drug dependency."
The 9-0 decision was a rebuke of the Harper government's tough-on-crime agenda and a precedent-setting ruling on the division of federal and provincial powers.
The court ordered the Harper government to abandon its effort to close the Insite facility in Vancouver.
The justices also told the government to grant an exemption to protect Insite staff from prosecution for drug possession or trafficking charges.
Aglukkaq also said she wants to review the decision.
Groups which backed Insite, including the Canadian Medical Association, said they were delighted by the ruling.
The justices agreed with the facility's supporters, who argued that closing the facility would violate the rights of addicts living in one of the country's most squalid neighbourhoods.
The ruling rejected the federal argument that the facility fosters addiction and runs counter to its crime-fighting agenda.
In 2008, two years after the Conservatives won power, then-health minister Tony Clement said the exemption which protects Insite staff should not be continued.
The court disagreed sharply.
"This limit is not in accordance with the principles of fundamental justice," Chief Justice Beverley McLachlin wrote on behalf of the unanimous court.
"It is arbitrary," she wrote. "It is also grossly disproportionate: the potential denial of health services and the correlative increase risk of death and disease to injection drug users outweigh any benefit that might be derived from maintaining an absolute prohibition on possession of illegal drugs on Insite's premises."
Insite supporters said peer-reviewed studies found the facility prevents overdose deaths, reduces the spread of HIV and hepatitis and curbs crime and open drug use.
The federal government rejected that evidence, arguing that Insite fosters addiction and runs counter to its anti-crime policies.
McLachlin made clear in the ruling that the federal government has a right to set policy, but when policy is translated into state action and law the courts must determine their validity under the charter.
"The discretion vested in the minister of Health is not absolute; as with all exercises of discretion, the minister's decisions must conform to the charter."
The ruling represents a significant setback for the Conservative crime agenda and could lead to the creation of other safe-injection sites in major cities.
The political ramifications of the decision quickly resonated well beyond the borders of Vancouver's troubled Downtown Eastside.
New Democrat MP Libby Davies, whose riding includes Insite, immediately called on the Harper government to abandon its ideological opposition to the facility.
"I don't believe any of them ever went there, they never took the time to really find out what Insite was about," she said.
"They always took this political, partisan, ideological position. And I want to say to them, have you now understood and learned the importance of what Insite is about, and how it's so much a part of our community?"
Liberal health critic Hedy Fry, who as a cabinet minister was involved in the early stages of what became Insite, said the ruling shows that a get-tough approach is the wrong way to deal with addiction.
"Addiction is a medical problem and requires medical and public health solutions," she said. "As a physician I believe that to deny proven, life-saving assistance to those who are vulnerable simply because one disapproves of their lifestyles is the ultimate immorality."
The president of the Canadian Medical Association said he was pleased with the ruling.
"Insite worked," said Dr. John Haggie. "It saved lives and it's a proven tool in management of addiction. We would like to see it as part of a national strategy.
"Canada's physicians have wanted to see something like this. It's evidence-based and the decision was fairly clear that in a situation where there is clear medical evidence of benefit and no negative impact in terms of public safety, the federal government had to grant an exemption."
Haggie said the ruling could pave the way for similar sites in Montreal and Toronto.
The Canadian Public Health Association applauded the decision, saying Insite and its programs provide a comprehensive approach to the health needs of people who use injection drugs.
"Addiction-related drug use is a health issue and not a criminal justice issue," said Debra Lynkowski, the association's CEO.
Dean Wilson, a plaintiff in the court challenge and a former addict from the Downtown Eastside, said he wants to work with the Harper government to get on with the business of saving lives.
"I'm just extending an olive branch," said Wilson, who says he has been clean for two years, after 44 years of addiction. "I want to continue to work together to do the best medical interventions we can. We're talking about really seriously ill people; we're not talking about people partying.
"I'm sure there's some ideology that we've got to try to work around but the bottom line is: Let's just save some real sick people's lives. And save some money at the same time, my goodness."
Dr. Julio Montaner, director of B.C. Centre for Excellence in HIV/AIDS, said it would be "very ill-spirited" if the federal government tried to defy the ruling by passing a new law.
"I think the outcry on the part of the Canadian public would be absolutely devastating to the cause."
Mark Townsend, of the Portland Hotel Society, which operates Insite, told a Vancouver radio station that he believes many Conservatives support the facility.
"But it was, unfortunately, a Stephen Harper thing," he said. "So that is exciting, that there is hope for people. We can beat the man when it's the right thing to do."
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