Bernard Valcourt, the minister responsible, made the announcement in a one-page statement Wednesday, saying the cuts were needed to streamline operations.
Valcourt said the agency has identified $15.2 million in savings through cuts and other measures, such as reducing travel and hiring fewer consultants.
"This is simply sound management and is now the norm for how government does business to ensure respect for taxpayers' money," he said in the statement.
Just over 100 employees with the agency received letters saying their position could be cut, but a department official insisted that no more than 42 people would lose their jobs.
She said fewer than 42 public servants could be cut if some retire.
Jeannie Baldwin of the Public Service Alliance of Canada said ACOA is losing 12 positions in Moncton, N.B., two in Nova Scotia and five in Ottawa.
Baldwin said she was receiving calls throughout the day from concerned staff.
"They're devastated," she said in Halifax. "What this government should be doing is stimulating the economy by creating jobs, not eliminating jobs."
Robert Chisholm, a New Democrat MP from Nova Scotia, issued a statement blasting the Conservative government for their latest round of cuts to the public service.
“This is just the latest example of Stephen Harper's Conservatives abandoning Atlantic Canada," Chisholm said.
"They have cut search and rescue, the Department of Fisheries and Oceans and now ACOA. The East Coast is clearly an after-thought for this administration."
For the fiscal year 2011-2012, the agency's funding was $317.9 million. That's expected to drop by $2 million in the next fiscal year.
ACOA was established in 1987 to stimulate Atlantic Canada's economy. It employs 718 people.