The Department of Foreign Affairs says all non-essential staff and all 29 dependents of the workers and diplomats there have been relocated from the mission in the capital of Bamako.
The situation in Mali has been volatile for nearly a year, with Islamist radicals taking over northern parts of the country following a coup.
Two thousand French troops are now stationed in the country, trying to help the government there dislodge the insurgents.
Foreign Affairs warns that it now has a skeleton staff in Bamako, with limited ability to help any Canadians who have stubbornly remained in the country.
The department says in addition to the political instability and military clashes, there is a threat of terrorism, banditry and kidnapping in the northern region.
Canada has sent a heavy-lift plane to help the French military with their operation in Mali.
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