Two of the border crossings are in Quebec and the third is in Saskatchewan. The country's Border Services Agency also reduced the hours three other border crossings in Quebec will be open, the Canadian Broadcasting Corp. reported.
The agency projects the changes will save $2.35 million a year.
The move doesn't sit well with some Canadians.
"The less human personnel you have controlling the border, the less adequate border protection," Pierre Pelland, mayor of Sutton in Quebec's Eastern Townships, said.
Some area residents have rallied and petitioned for the decision to be reversed.
The CBC said a recent report from the Integrated Border Enforcement Team, which is comprised of Canadian and U.S. law enforcement officials, found unguarded roads between Quebec and the United States are used by drug traffickers and those smuggling people across the border.
The Border Services Agency said it will put up barriers and cameras at the former checkpoints to deter illegal migrants from crossing there.
The three closed checkpoints are at Franklin Centre, Jameson's Line and Big Beaver. Those with reduced hours are at Morses Lines, East Pinnacle and Glen Sutton.