The Conservative government served notice to 700 Agriculture Canada employees last week that their jobs are in jeopardy.
Unions said more than 400 jobs will be lost to cost cutting.
Research, innovation, technical support and policy analyst positions were heavily targeted.
Critics said the cuts show a disturbing disregard for basic research within the department.
The Professional Institute of the Public Service of Canada said of the 350 employees who were targeted with letters of potential job loss, 79 are scientists, 76 are information specialists, 14 are biologists and five are research managers.
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The targeted positions are concentrated in the Ottawa region but extend across the country.
Within Agriculture Canada, the last vestiges of the Rural Secretariat are on the chopping block.
Among members of the Canadian Association of Professional Employees, 96 employees received letters that their jobs are targeted, although 17 have decided to leave the public service and the rest will compete for remaining jobs.
CAPE represents economists and policy analysts.
Proposed cuts extend across the Prairies, while in British Columbia, staff at Agriculture Canada’s range management centre in Kamloops have been targeted.
“I think they are in the process of gutting the basic research that Agriculture Canada does that is the future of the agriculture industry,” Public Service Alliance of Canada agriculture union president Bob Kingston said.
“They really don’t seem to get the importance of research.”
At least 250 positions will be lost among his members.
Ron Bonnett, president of the Canadian Federation of Agriculture, said the job cuts are disturbing.
“We knew cuts were coming, but these seem to be coming without a real vision of what is needed,” he said.
“It makes us nervous that there seems to be no vision, no overall plan about how research, basic research, should be funded.”
Bonnett said the government concentration on short-term and industry directed research projects is useful, but there must be a broader vision.
“What we’re seeing is government pulling back from A-base (fundamental research) funding and going forward on a project-by-project basis,” he said.
“We need more vision than that.”
Agriculture minister Gerry Ritz dismissed the criticisms in the House of Commons last week.
New Democrat Mathieu Ravignat said Agriculture Canada is walking away from science, which is “akin to turning back the clock.”
Ritz said he had it wrong.
Instead, the department is cutting costs in information technology services, personnel, asset management, policy “and a lot of things that are duplications of what are being done by industry and by the provinces.”
He said the intent is to make the department more efficient so it can serve the industry better.
“We are looking at an efficient, effective system that builds the strength of the farmgate,” Ritz said.
“That is exactly what we are delivering.”
Bonnett said the CFA will meet with Ritz and agriculture committee chair Merv Tweed from Brandon to urge the committee to study the impact of cuts and government priorities on essential public research.
“It seems the research agenda is to be dictated by industry for short-term projects, but I think we need a longer-term perspective as well,” he said.
Deputy minister Suzanne Vinet said in a memo to Agriculture Canada employees May 9, the day the job loss letters were delivered, that the cuts are for the good of the department and the industry, and the targeted employees have been important.
“We want to express our gratitude for the high level of performance and dedication employees have shown throughout what has been a challenging period in our evolution,” she wrote.
