All federal departments using software vulnerable to the so-called Heartbleed bug have been ordered to immediately disable public websites.
The directive issued late Thursday calls this a precautionary measure until the "appropriate security patches are in place and tested" but did not indicate how many departments are involved.
The government's Chief Information Officer says in a statement issued through the Treasury Board that while disruptive, "this is the best course of action to protect the privacy of Canadians."
The statement adds that until measures are applied, "Canadians will be unable to access certain Government of Canada websites."
The Heartbleed bug is caused by a flaw in OpenSSL software, which is commonly used on the Internet to provide security and privacy.
The bug is affecting many global IT systems in both private and public sector organizations and has the potential to expose private data.
The Canada Revenue Agency had shut down its online filing services on Wednesday and said it hoped they would be up and running again by the weekend.
CRA services affected included tax-filing systems E-file and Netfile, as well as access to business and personal account data stored by the system.
Taxpayers were assured they would not be penalized if they were prevented from filing a return on time because of the shutdown.
The Canadian Bankers Association had said online banking applications of Canadian banks were not affected by the bug.