The decision follows a review by Canada's chief information officer, and the app "presents an unacceptable level of risk to privacy and security", a government spokesperson said in a statement.
A TikTok spokesperson said the company was disappointed by the decision.
It comes just days after the European Commission announced a similar ban.
Prime Minister Justin Trudeau said there was enough concern about security around the app to require the change.
"This may the first step, this may be the only step we need to take," he said on Monday at a press conference near Toronto.
TikTok has been criticised for its use of personal information and ties to the Chinese government.
The short-form video app is owned by Chinese firm ByteDance Ltd.
US federal employees were banned from using TikTok late last year, and on Monday the White House gave government agencies 30 days to scrub the app from their systems.
A number of American universities have banned the app from being used on their networks. Broader public bans have been implemented in India and several other Asian countries.
The company insists that Chinese government officials don't have access to user data and that a Chinese version of the app is separate from the one used in the rest of the world. But last year, the company admitted some staff in China can access the data of European users.
The ban for European Commission employees is set to come into force on 15 March.
Canadian privacy regulators are also investigating TikTok over concerns about user data, in particular whether the company obtains "valid and meaningful" consent from users when collecting personal information.
About a quarter of Canadian adults use the app, according to a recent survey by researchers at the Social Media Lab at Toronto Metropolitan University.
In a statement, Mona Fortier, the president of Canada's Treasury Board, said the government "is committed to keeping government information secure".
The app will be removed from government-issued phones this week and other devices and blocked from downloads in the future.
"On a mobile device, TikTok's data collection methods provide considerable access to the contents of the phone," Ms Fortier said. "While the risks of using this application are clear, we have no evidence at this point that government information has been compromised."
The Treasury Board, which oversees the operations of the federal government, includes the country's chief information officer.
In a statement, a company spokesperson said the ban on government-issued devices happened "without citing any specific security concerns about TikTok or contacting us to discuss any concern prior to making this decision".
"We are always available to meet with our government officials to discuss how we protect the privacy and security of Canadians, but singling out TikTok in this way does nothing to achieve that shared goal," the spokesperson said.
"All it does is prevent officials from reaching the public on a platform loved by millions of Canadians."