"I spoke with my mom, and thankfully she's doing fine," the prime minister said in a Twitter message thanking fire and ambulance crews "for their incredible work."
"I'm keeping the other families affected by this fire in my thoughts today," he added.
Trudeau's office did not immediately respond to requests for more information.
But public broadcaster Radio-Canada said Margaret Trudeau, who is also the widow of late prime minister Pierre Trudeau, was treated in hospital for smoke inhalation and possibly burns. She is expected to recover.
The blaze reportedly started on a fifth floor terrace, and took 70 firefighters to douse. Three families were evacuated.