The Anonymous online collective claimed responsibility for the attack — which shut down several federal sites and played havoc with email — as a protest against the recent passage of the federal anti-terrorism bill.
Early Wednesday afternoon, Treasury Board President Tony Clement tweeted that until full service was restored, the public should use 1-800-OCanada.
Several hours of government silence on the incident, known as a denial of service attack, followed.
The federal Cyber Incident Response Centre, which routinely publishes alerts and advisories, posted nothing about the events.
"We are working on restoring services as soon as possible," said a brief, late-afternoon statement from Dave Adamson, the government's acting chief information officer.
"We continue to be vigilant in monitoring any potential vulnerabilities."
Denial-of-service attacks, which bombard a site with traffic, are a common means of shutting down a web server.
Anonymous has carried out cyberattacks against governments, corporations and others in the name of free speech, Internet liberties and anti-capitalist causes.
There was no immediate confirmation that the loosely knit coalition was actually behind the assault on federal sites.
However, Blaney said there were no excuses for such an attack, noting "law-enforcement agencies" were looking into the matter.
"We are living in a democracy," Blaney said. "And there are many ways to express your views."
The incident follows a high-profile hacking of the National Research Council last year — an episode the federal government blamed on a Chinese state-sponsored player. Beijing has denied involvement, accusing Canada of making irresponsible accusations.
Assaults that crippled computer systems at the Finance Department and Treasury Board in 2010 were linked to efforts — possibly originating in China — to gather data on the potential takeover of a Canadian potash company.
The government stresses it has since invested energy and millions of dollars in a national cybersecurity strategy.
"Cybersecurity is an issue that we take very seriously," Blaney said.
Follow @JimBronskill on Twitter