Others sections are also being warned of position changes or eliminations.
There's been speculation about the habitat management branch since the words "habitat protection" were eliminated from Canada's Fisheries Act.
About 30 people work in DFO's habitat management branch in Nova Scotia, reviewing projects on or near water to preserve fish habitat.
"Everybody in habitat received an affected letter, which means that they could wind up being surpluses," said Bob Ellis, regional vice-president of Local 80166 for the Union of Environment Workers.
Letters were also sent wholesale to other sections at the department's Dartmouth office, according to Ellis.
"Finance and compensation advisers, the whole department, both departments are moving to New Brunswick," Ellis said.
Administrators are being relocated as part of centralization, but it's not clear what will happen with the habitat employees.
Earlier this week scientists staged a protest in Ottawa, claiming federal layoffs and other environmental changes mean a 'death of evidence.'
"We've increased expenditures on research and development in areas, including the Canadian Foundation for Innovation," Michelle Rempel, the parlimentary secretary to the Minister of Environment, said earlier this week.
DFO managers have told Ellis they don't yet know how the department will manage habitat in the future.
"Hopefully we're not going to lose anybody," Ellis said.
Claire Dansereau, DFO deputy minister, delivered the government's message at a town hall at the Bedford Institute of Oceanography Wednesday.
Staff were told the focus is on commercial fish species and the department will get its science data from academics, Ellis said.
"If we are going to be funding research outside the department, why is the department not doing it," he said.
DFO said it's cutting 130 habitat positions across Canada and keeping 75 per cent of current habitat management staff across the country.
The department wouldn't confirm that every habitat employee received the letter, citing privacy.