Department websites that were hit include the Justice Department and Canada's spy agencies CSEC and CSIS.
The website for the Senate of Canada was still out of service as of 3 p.m. ET.
Treasury Board President Tony Clement confirmed to CBC News that the government's servers were hit with a denial of service attack.
"I can tell you, I've just been through a briefing on it. There has been an attack on Government of Canada servers, GC servers. It is as a result of a, of a — what we would call a cyberattack," he said.
He urged users to call 1-800-OCanada for help until full service is restored.
When CBC News phoned this number, the service operator was unaware of the interruption.
"Public Safety and of course Shared Services Canada are working to restore service," said Clement. "But in the meantime, we're working very diligently to restore services as soon as possible and to find out the origination of the attack."
The online hacker group Anonymous has claimed responsibility for the attack, in protest against the recent passing of the government's anti-terror Bill C-51.
"Do we trade our privacy for security? Do we bow down and obey what has become totalitarian rule? Don't fool [yourselves]," the group wrote in an online post.
"The Harper regime does not listen to the people, it acts only in [its] best interests."