Union officials say a dozen researchers and experts who work on mental-health issues in the military have been told their jobs are on the line.
The Opposition called the cuts callous, given statistics released this week showing suicide rates among soldiers reached record high levels last year.
But Defence Department officials say no final decision has been made on those positions. Meanwhile, they're moving to increase the number of front-line personnel available to help active soldiers and veterans.
"Our government has made the decision to ensure that the positions of all front-line workers who treat ill and injured personnel are protected," Defence Minister Peter MacKay said in a statement.
"Direct patient care is not being affected in any way by recent efficiency measures."
Beefing up the military is a key plank of the Conservative government, which has been particularly sensitive to criticism of departments that serve soldiers.
The Defence Department took the biggest hit in the March federal budget, trimming more than $1 billion in spending over the next three years.
Union officials say that means thousands of civilians who support the work of the military will lose their jobs and the resulting work will fall on the shoulders of soldiers.
The unions, representing civilian professionals and academic experts within the department, said the cuts will hurt mental-health services.
They said about a dozen researchers who focus on monitoring rates of post-traumatic stress disorder and concussions are being told their jobs are on the line.
"Monitoring the health of Canadian Forces members is not merely optional for DND," Claude Poirier, president of the Canadian Association of Professional Employees, said in a statement.
"Because Canadian Forces members are generally excluded from health surveys conducted by Statistics Canada, DND studies are essential to identify health issues affecting military personnel, and to target areas for intervention."
New Democrat MP Jack Harris said he takes no solace from MacKay's promise that resources are being increased.
He said the increases are pegged to 2006 resource levels and since then there's been an unanticipated rise in the number of soldiers seeking assistance.
"There's a real hypocrisy here between their statements on the one hand, trying to whip up support for their policies, but at the same time neglecting the basic needs of Canadian Forces members and veterans," Harris said.
Statistics released by the military this week show 20 soldiers died by suicide in 2011, the year that marked the end of the combat mission in Afghanistan.
In 2010, 12 soldiers took their own lives.
The Military Police Complaints Commission is currently reviewing the 2008 suicide of a soldier, examining in part how the military handled his mental health in the weeks before he died.