The department is bracing for a $79.3-million decrease in funding over the next three years as part of Ottawa's cost-cutting measures. Officials have said research will still be done, though it will be refocused on what it says are areas that directly support conservation and fisheries management.
Federal scientists losing their positions say they aren't permitted to publicly discuss the cuts, but their colleagues in academia say valuable knowledge could be lost, posing threats to the country's environment and its competitiveness.
"These scientists have an incredible number of years of experience working on a particular topic," says Elizabeth Boulding, a molecular ecologist at the University of Guelph.
"When I go in there with a project, we can get a lot more done in three or four years than we could possibly do without their assistance."
Boulding cites as an example her work with Brian Glebe, a biologist at the Fisheries Department's research centre in St. Andrews, N.B., whose position will be cut following a program review last year. For seven years, they have worked to identify genes in salmon that resist infectious salmon anemia, a virus that can kill up to 90 per cent of the salmon it infects, depending on the strain.
They are also seeking the genes of salmon resistant to sea lice infestation with the goal of breeding those fish.
"This worries me a great deal because I can't do this work myself," Boulding says. "There doesn't seem to be any plan to replace him.
"It makes me nervous about writing another grant to do this work because I don't know who else can do this work."
Glebe's job is to introduce the diseases to salmon in quarantined pens. He said he's uncertain of how much longer he'll be able to stay on in his post, and referred other questions to the department's communications staff.
Boulding said Canada runs the risk of falling behind other countries such as Norway, where the public sector is doing similar work with its aquaculture industry.
"If they have disease-resistant salmon and we don't, how will we be competitive?" Boulding said.
Dave Gillis, director general of the ecosystem science directorate at the Fisheries Department, said the decision to cut Glebe's position and other more recent budget reductions came after careful review.
"The number of subject areas that the program was to focus on has been reduced and it no longer includes the subject area that Dr. Glebe was working on," he said in a telephone interview.
Gillis said he doesn't know whether others would continue Glebe's work.
"It's a case-by-case situation," he said.
Other university scientists are also alarmed by the department's decision to end its support of the Experimental Lakes Area water monitoring project in northwestern Ontario. The 44-year-old program covers 58 small lakes and is used by scientists to conduct real-world experiments on entire ecosystems.
A group of university scientists and students trying to save the project says research done there has altered environmental policies across the continent, prompting mercury emissions rules for coal-fired power plants, a ban on phosphorus in detergent and action on acid rain.
David Schindler, an ecologist at the University of Alberta, is among a network of university professors opposing the cut.
"The Experimental Lakes Area is probably Canada's most famous scientific facility," he said in an email.
"Doesn't it seem foolish for a country that seems to have chronic anxiety about its international stature to close such a facility?"
Gillis said the department is attempting to find universities to take over research stations, but added he can't be specific about how or when that will happen.
"We are going to work with the science community to find an alternate operator for the site," he said.
"We are aware that there are a number of universities and other agencies that either work there directly or fund work there. So, we will very shortly be initiating discussions with the various elements of that community to seek their interest."
Cuts have also struck the Bedford Institute of Oceanography in Halifax, the country's largest ocean research centre. The institute's Centre for Offshore Oil, Gas and Energy Research will stop some of its work, though Gillis said an advisory group of outside scientists will be given funds to continue research on the biological effects of contaminants.
But Jeff Hutchings, a biologist at Dalhousie University, says he has concerns about that approach.
"Advisory groups do not undertake research. They advise," Hutchings said in an email.
"This group is no replacement for dedicated scientists embedded within a dedicated government science program. This news bears all the transparent hallmarks of the stop-gap measure that it is and the utter absence of leadership that it represents."
Gillis said he can't say precisely how many science jobs have been cut in the latest round of budget cuts.
The department's annual budget is $1.4 billion.