The Canada Revenue Agency is hoping its online filing services will be up and running again on the weekend.
The agency locked down the system yesterday because of the so-called ``Heartbleed'' computer bug.
The shutdown came after the Canadian Cyber Incident Response Centre issued a warning to system administrators about the coding flaw.
Other federal systems were also being assessed for their vulnerability to the threat.
CRA services affected by the outage included the electronic tax-filing systems E-file and Netfile, as well as access to business and personal account data stored by the system.
The agency says the revenue minister has given assurances that taxpayers would not be penalized if they are prevented from filing a return on time because of the shutdown.
The Canadian Bankers Association says online banking applications of Canadian banks were not affected by the bug.