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.
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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."
Treasury Board president Tony Clement confirmed the directive in a tweet early Friday morning.
I have approved a directive to DISABLE all Government of Canada public websites running on unpatched Open SSL due to #heartbleed threat.— Tony Clement (@TonyclementCPC) April 11, 2014
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.
However, it's not clear the extent to which other federal government systems were affected. Employment and Social Development Canada, which handles things like Employment Insurance and Canada Pension Plan, Social Insurance Numbers and passports, had issued a statement Wednesday saying its web applications do not use OpenSSL and are therefore not affected.
"We have also worked with Shared Services Canada to confirm that none of our other connectivity solutions were affected," the department said in a statement emailed to CBC News.
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 and new applications for a record of employment. Taxpayers were assured they would not be penalized if they were prevented from filing a return on time because of the shutdown.
In the meantime, Canadians using commercial tax software may need to change their passwords, as some programs such as Turbo Tax were affected by the bug.
The Canadian Bankers Association had said online banking applications of Canadian banks were not affected by the bug.