The Conservative government is moving to permanently strip control of the Public Health Agency of Canada's budget and staff from the chief public health officer, a step critics fear could diminish the clout of the country's top doctor.

The proposed changes, which are tucked into Ottawa's most recent omnibus budget bill, would make the top doctor an "officer" who would keep providing scientific advice to the health minister but who would no longer be deputy head of the agency.

That role would now be carried out by a president, a new post that Prime Minister Stephen Harper has already recommended be filled by Krista Outhwaite, the civil servant who led the agency while the government left the chief public health officer job vacant for 16 months.

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Health Minister Rona Ambrose says the idea for the new structure came from the agency itself and that it "makes a lot of common sense" to permanently relieve the busy top doctor, Gregory Taylor, of the burden of overseeing 2,500 employees and a $615-million budget.

The change would leave him to concentrate on the rest of the job's original mandate, namely providing public-health advice to the government, delivering health messages to Canadians and co-ordinating with provinces and international health bodies, as he has done recently in preparing the country for potential cases of Ebola.

"He will focus primarily on communicating and engaging in public-health issues," Ms. Ambrose said.

But some in Canada's public-health community worry that if the chief public health officers loses control of the staff and purse strings for good, he could lose control of the agenda, too.

"Our understanding of the change is that the chief public health officer will no longer have the authority to direct the resources of the agency either in an emergency situation or just in regular times," said Ian Culbert, the executive director of the Canadian Public Health Association, a national not-for-profit organization representing public-health professionals. "So the concern is, will administrative or bureaucratic priorities overrule public-health priorities?"

Both the Public Health Agency of Canada and the job of chief public health officer were created after Canada fumbled its handling of the 2003 SARS outbreak, which killed 44 people in this country.

The federal Liberal government of the time considered several different models for the top doctor job, but settled on making the successful candidate the deputy head of the agency – the health minister is the head – because of the control and power it would lend the new position, according to Carolyn Bennett. The Liberal MP and former minister of state for public health was tasked with getting the new agency up and running.

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"It was [supposed] to be an agency head with the expertise that could go downtown and get the money and be able to set the priorities," Dr. Bennett said of the chief public health officer's role. "Anybody I've talked to about [the proposed changes] in the public-health community has the same two words: bad news."

The public-health agency, however, says Dr. Taylor disagrees with that assessment. "Dr. Taylor is very supportive of these changes," a spokesman for the agency said by e-mail. Dr. Taylor was not available for an interview

He became the acting chief public health officer after David Butler-Jones, the first person to hold the job, suffered a stroke in May, 2012 and formally stepped down in June of 2013. Ms. Outhwaite, who is not a medical doctor, was temporarily made deputy head of the agency in May 2012, a post she has held since.

Dr. Taylor, meanwhile, was officially elevated to the role of chief public health officer on Sept. 24. Under the existing legislation, that job is still designated as the agency deputy head. In an interview with The Globe and Mail that day, he said the stopgap approach of running the agency in co-operation with Ms. Outhwaite had been working very well.

Joel Kettner, a former chief public-health officer of Manitoba and now the medical director of the International Centre for Infectious Diseases in Winnipeg, pointed out that the proposed new model, in which a doctor provides scientifically based public-health advice while a bureaucrat runs the department, is similar to the arrangements in most provinces and territories in Canada.

"I think that, in and of itself, this could be a good change," Dr. Kettner said.

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It is unclear if making the temporary arrangement at the Public Health Agency of Canada permanent might affect the widely respected Dr. Taylor's ability to speak freely to Canadians. Since his appointment, he has appeared alongside Ms. Ambrose at several news conferences on Ebola, taking questions and offering calm and common-sense advice about the virus.

The exception to that has been the government's controversial decision to stop processing visa applications from the three West African countries hardest hit by Ebola, a move that the World Health Organization says is not supported by the science and runs afoul of International Health Regulations.

Dr. Taylor has not spoken publicly on the matter and the Public Health Agency of Canada has referred all questions about the policy to Citizenship and Immigration Canada, which oversees visa rules.

"The person I would most like to ask about this situation is the chief public officer," said Steven Hoffman, director of the Global Strategy Lab at the University of Ottawa. "He's a public-health professional. Does he think there's a good public-health justification for this?"

Asked if Dr. Taylor had provided advice on the issue privately to the government, the Public Health Agency of Canada spokesman referred the question to a spokesman for Citizenship and Immigration who resent a two-day-old statement on the visa policy and ignored the question.

"I can't give you that information," Ms. Ambrose said at a news conference in Edmonton this week. "All those conversations are private and this was the result of a number of discussions at the cabinet table."

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When it comes to the formal changes to the top doctor's role, Libby Davies, the NDP's health critic, said that at the very least, the changes deserve full scrutiny as a piece of separate legislation.

"To bury it in an omnibus bill says to me that they don't want people to know about it and they don't want questions."

With a report from Justin Giovannetti in Edmonton