The left-leaning think-tank predicted Tuesday that 4,400 full-time jobs will be lost in the region by March 2015 — about nine per cent of the region's federal workforce, not including Crown corporations.
The report says that's unfair because the Harper government has promised to cut only 4.8 per cent of the entire federal public service, which includes about 400,000 employees.
However, the centre says hard numbers are difficult to come by because Ottawa has released very little information since announcing its plans.
"There's a real lack of transparency and accountability," said Christine Saulnier, co-author of the report and director of the centre's Nova Scotia wing.
"We put in a request to Treasury Board and we got back a letter asking for money. We have yet to see any information from that request."
Saulnier said the group contacted 30 regional directors within the Atlantic bureaucracy to collect data, but only four consented to be interviewed.
The centre says that more than 2,100 federal workers in the region have already received notices telling them their jobs could be affected, but it remains unclear how many have actually lost their jobs.
The Conservative government has said it will cut 19,200 jobs over the next three years with about 37 per cent to be eliminated through attrition. But the centre says its research suggests the actual number will be much higher, given the budget-cutting targets already on the table.
Andrea Mandel-Campbell, a spokeswoman for Treasury Board president Tony Clement, issued a statement saying the centre's report was "bunk."
"We have always said that every region will retain its proportion of federal jobs and that remains the case," she said in an email.
"The CCPA is not a non-partisan, independent think-tank, but a tool of the NDP used to sow political division and misinformation. It's obviously a biased report and huge union influence is proof of that."
Mandel-Campbell said just under 11,000 federal jobs have been cut since March, mostly through attrition.
She said the centre was wrong to point to the total workforce reduction of 4.8 per cent. She said the federal government is making sure that each region's existing share of federal employees remains the same as the overall number drops.
The spokeswoman also says the report overstates the impact of job losses in the Atlantic provinces.
For instance, she says the reported reductions for Veterans Affairs in Atlantic Canada are 46 per cent higher than the total national reduction in full-time equivalent positions for the agency.
Gary Corbett, president of the Professional Institute of the Public Service of Canada, said the cuts have already had an impact on the Canadian Coast Guard's regional environmental response teams, which co-ordinate the cleanup of oil spills and other disasters.
"Are you really going to fly in someone from Montreal to do that?" he asked. "You really need the knowledge here to do it."
Corbett said he understood that the federal government has to cut costs, but he insisted the process of trimming jobs shouldn't be done under a cloak of secrecy and without input from those affected.
According to the centre, Nova Scotia will lose 1,600 federal jobs by 2015, New Brunswick 1,100 positions, Newfoundland and Labrador 419 and P.E.I. 446. Another 800 jobs could be transferred outside the province, but the report says there's no way to determine the final number.
By far the biggest impact is expected at the Department of National Defence, where an estimated 1,300 jobs will be lost, almost all of them in Nova Scotia, the centre's study said.
Saulnier said the average income for a federal employee in Atlantic Canada is about $67,000 annually.
"That's a significant amount of income that will be lost in those communities," she told a news conference at a Halifax hotel.
"It will have a disproportionate effect, not just because we have more cuts here, but because we are the region least able to absorb those cuts" because of higher unemployment and rural residency rates.