Montreal police responded to emergency calls at 1am on Monday after a Molotov cocktail was thrown into the building on Décarie Boulevard near Vézina Street.
The firebomb was flung into the building through a front door glass window and it exploded in the hallway, causing a carpet to catch fire.
But no one was injured in the attack, said Rabbi Saul Emanuel, the head of Montreal’s Jewish Community Council.
“No one was present and minimal damage occurred,” he said.
“The rise in antisemitism in our city is frightening and the repeated violence and attacks on our community are abhorrent and condemned in the strongest terms,” he added.
Mr Trudeau called the attacks “deplorable and unacceptable” in a tweet on Tuesday.
“I strongly condemn the attack on the Jewish Community Council of Montreal building yesterday. These continued acts of antisemitic violence are deplorable and unacceptable – and must stop immediately. We must all stand united against such vile, hateful acts,” he said.
The incident comes amid a spike in attacks on both Jewish and Muslim communities in Europe and America amid the intense bombardment of Gaza by Israeli forces in response to the 7 October attack by Hamas militants.
Two Jewish schools in Montreal were targeted at night by gunfire earlier this month. One of the schools was attacked twice.
A synagogue was also firebombed in the suburb of Dollard-des-Ormeaux, sparking a small fire.
Law enforcement in Montreal and Toronto, cities with significant Jewish populations, have issued warnings about a recent increase in hate crimes, specifically noting a rise in antisemitic incidents