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Ottawa is circumventing Ontario’s new restrictions on supervised drug consumption, allowing cities and harm-reduction groups that want to open sites to prevent overdoses to apply directly to Health Canada, with the federal government committing to help them get the funding as a way to battle the country’s opioid crisis.

The Ontario government announced in October it would limit the number of supervised-consumption sites in the province to 21. Only two of the 10 areas in Ontario with the highest number of opioid-related deaths in 2017 have sites, according to data from Public Health Ontario.

“I think that we have to recognize and we have to be very clear with Canadians: Supervised-consumption sites save lives," Health Minister Ginette Petitpas Taylor said in an interview on Thursday. “We as a federal government want to ensure that we remove all barriers, cut the red tape.”

The Public Health Agency of Canada revealed earlier this week that more than 2,000 people have died as a result of opioids so far this year, a slight increase over the same period last year, and an indication the crisis is not under control. Many of the deaths involve the powerful painkiller fentanyl. Public-health experts say supervised-consumption sites are crucial because they provide people with a safe place to use drugs, as well as access to some health services and help if they overdose.

Until recently, the federal government was responsible for granting the exemptions from the Controlled Drugs and Substances Act that allowed the sites to open. But late last year, Ottawa said it would let provinces offer exemptions so they could quickly set up sites in areas where the need was greatest.

In October, the Ontario government also rebranded supervised-consumption and overdose-prevention sites as “consumption and treatment services” and said operators of existing ones would have to apply to the province to stay open and receive funding. It is unclear what the federal change will mean to these facilities.

While provinces fund health services, Ms. Petitpas Taylor said the federal government can work with municipalities and not-for-profit organizations to ensure they receive the money to operate.

“There’s always other ways,” she said. “We want to make sure that there’s no barriers in place.”

Ontario Health Minister Christine Elliott declined an interview request. Hayley Chazan, a spokeswoman, said in a statement the province has put in place a program “to get those who are struggling with addiction the help they need.” The statement added that the new consumption and treatment services model will focus on connecting people to health care, treatment and rehabilitation.

The statement did not address the federal changes.

Thomas Kerr, a professor in the department of medicine at the University of British Columbia who studies safe-consumption sites, called the federal decision an important and necessary step to ensure people in Ontario have access to overdose-prevention services.

“We are in the midst of one of the worst public-health crises in modern history, the opioid epidemic,” Dr. Kerr said. “The Ontario government is putting up ideological barriers to the implementation of a life-saving intervention.”

Sarah Ovens, an organizer with the Toronto Overdose Prevention Society, said Ontario’s move was unnecessary, and that the federal changes may help improve access.

“Any effort by the federal government to remove those barriers and to help people and organizations and municipalities work around that red tape is needed and is good news,” she said.

Nick Boyce, director of the Ontario Harm Reduction Network, said the federal move is a positive step, but that much more needs to be done. He singled out decriminalization of drugs as one of the most important measures that could help reduce the number of people being harmed and dying from opioid use.

“It’s all Band-Aids until we fix the underlying problem,” Mr. Boyce said.

Ms. Petitpas Taylor said the federal government is not considering decriminalization at this point, and that no one measure will solve the crisis.