In a statement, Justin Trudeau's office said that the Prime Minister and Boissonnault have agreed that the minister will step away from the cabinet effective immediately, Xinhua news agency reported.
"Boissonnault will focus on clearing the allegations made against him," the statement said.
Boissonnault has been facing scrutiny for months on his connections to a former medical supply business he previously co-owned as well as his past descriptions of his family's Indigenous history.
Veterans Affairs Minister Ginette Petitpas Taylor will take on Boissonnault's responsibilities, according to local media.