The Public Service Alliance of Canada said Wednesday that more than 5,500 civil servants have been given notice, including more than 250 who provide client services to military veterans.
Hundreds of policy analysts were also among those told that their jobs are on the block as the Conservatives seek to slash spending by $5.2 billion over the next three years.
The tension between the political and policy branches of government has been palpable since the Conservatives were elected in 2006, with perhaps the highest-profile case being the resignation of Canada's chief statistician over the decision to cancel the long-form census.
"What we've seen over the past little while is a change in what's expected of advisers," said Claude Danik, executive director of policy for the Canadian Association of Professional Employees, which represents more than 13,000 economists and social scientists who advise the government on public policy.
"In the past they wanted advice that was independent. We don't feel that's still what is being asked. It depends on the department but they're often told to find information that will support particular positions."
Danik says he doesn't see the cuts as political but they do raise a serious question: "How will departments be able to carry out their mandates with these cuts?"
A spokesperson for Treasury Board President Tony Clement said since the cuts only eliminate four per cent of the public service over the next three years, there will still be plenty of advice and support to go around.
"This government respects and appreciates the hard work that public servants do for this country," Jennifer Gearey said in an email.
"We have found fair, balanced and moderate savings measures to ensure jobs, economic growth, and long term prosperity for all Canadians."
According to PSAC, unionized employees in 23 federal departments received notice Wednesday, with 1,137 staff at the Canadian Border Services Agency notified their position could be on the hit list, and 689 such positions at Agriculture Canada.
The number of notifications doesn't represent the number of actual jobs that could be cut, union officials explained.
The system requires all employees who do a particular job to be notified no matter how many of their positions are being eliminated.
Geographically, Ottawa bore the biggest brunt with 2,224 workers put on notice, according to the union.
Among the analysts told Wednesday that they'll be affected by the job cuts are those who work at Foreign Affairs, Treasury Board, and Health Canada.
Danik said it appeared many of the cuts at Health were coming from within the branch of the department that focuses on First Nation and Inuit health.
A spokesperson for the department couldn't say what programs are being cut because not all employees have been notified.
"We are still continuing to provide core health services to First Nations and Inuit," Stephane Shank said.
Other departments, including Treasury Board and the Privy Council Office, gave the same response when asked for more details about the cuts, refusing to confirm job numbers or programs under the knife because the notification process is ongoing.
But now that individuals are being told, the departments should come clean with the public on what programs are being affected, said John Gordon, national president for PSAC.
"I think they've been muzzled by the government," he said.
Almost all federal departments were told last month to slash their budgets by five per cent or more, meaning few will be immune from job cuts.
Others notified Wednesday include workers at the Canadian Space Agency, Environment Canada and the Canadian Food Inspection Agency.
Some 308 employees are being let go from the food inspection agency, the union said.
"With fewer independent food safety professionals working in the public interest, industry self-policing will increase and consumers will be left to fend for themselves," said Bob Kingston, president of the union representing food inspectors.
A spokeswoman for Agriculture Minister Gerry Ritz said the government is actually increasing resources for food safety, pointing to $51 million outlined in the budget.
"The Agency will not make any changes that would in any way place the health and safety of Canadians at risk," Meagan Murdoch said in an email.
She said one way the cuts will be achieved is by moving the grants and contributions programs into one office.
New Democrats said the cuts are putting Canadians at risk.
"These cuts are just another scary reminder that Conservatives care more about funding their backwards priorities rather than protecting Canadians' safety and trust in the food industry," said Malcolm Allen, NDP critic for Agriculture and Agri-Food.
As the cuts were being announced, the Harper government was trumpeting funds for a meat processing plant in Toronto.
"We will enhance food safety and traceability, improve plant efficiency, and reduce operating costs through the purchase of value-added equipment," David Schwartz, president of Quality Meat Packers, said in a statement included in the government's press release.
Altogether, about 19,200 jobs will be lost over the next three years following last month's budget.
Some workers could be reassigned, while others will be given the option of leaving early; about 7,000 of the job cuts reported in the budget will be due to attrition, the government said.
But PSAC has said the number is much larger.
A budget freeze in 2010 saw 9,700 positions lost and there are still 6,300 jobs that will be cut as a result of the 2007-2010 spending reviews, the union said.
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