Barbara Mottram, press secretary for Fisheries Minister Keith Ashfield, says workers may be asked to relocate or switch jobs but won't necessarily be laid off.
In an email, she says the cuts amount to less than two per cent a year over three years of the department's workforce of 11,000 staff.
She says the rate of people leaving through attrition, such as retirement, has been about six per cent a year.
The Public Service Alliance of Canada issued a news release Thursday saying that 1,072 workers received notices saying they could lose their jobs.
The union said the Canadian Coast Guard is hardest hit, with their workers receiving 763 of the notices.
"On the one hand we have a government putting on a show to celebrate the 50th anniversary of the Coast Guard, and on the other we see it closing offices and shutting down search and rescue," said Chris Aylward, the union's national vice president.
The union said finance and administrative workers, fisheries management workers and technicians who support biologists and chemists in hatcheries and research stations were among those who received notices their jobs could be effected.
A spokeswoman for the federal Fisheries Department says that the notices sent to employees are the first step in the process, and shouldn't be equated to job losses.
"Receiving a letter does not mean the employee will lose their job; it may simply be an indication that their sector or branch in the department is being changed or they may be asked to relocate or redeploy within the Fisheries Department or the government," wrote Erin Filliter.
She said the changes will reduce middle management and overhead, while Ottawa will ensure frontline operations are maintained.