The travel restriction will not apply to flight crews, diplomats, immediate family members of citizens and, for now, US citizens.
As of Monday, confirmed cases of the virus in Canada have reached nearly 400 with no reported deaths.
Reporters pressed the prime minister to explain why Americans are exempt from the travel restrictions as the number of cases below the border has surged to nearly 4,000, including at least 71 deaths.
Mr Trudeau suggested that the rule could change: "Everything is on the table to protect Canadians."
The prime minister addressed reporters while in self-isolation, which he imposed on Thursday following his wife Sophie's positive diagnosis of the virus.
He said: "I know that these measures are far-reaching. They are exceptional circumstances calling for exceptional measures."
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The border restrictions — which follow calls from provincial governments for a more aggressive federal response — will not apply to commerce or trade.
Last week, Parliament suspended sitting for five weeks after liberals unveiled a $1bn relief package to address Canada's health and economy, in addition to billions of dollars to support businesses that expect negative impacts in the wake of the pandemic.
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