Quebec City police confirmed to ABC News that the two suspects being held are men in their 20s.
Prime Minister Justin Trudeau called the shooting a "terrorist attack on Muslims," and offered his condolences.
“While authorities are still investigating and details continue to be confirmed, it is heart-wrenching to see such senseless violence. Diversity is our strength, and religious tolerance is a value that we, as Canadians, hold dear," Trudeau said.
Christine Coulombe of the Quebec Provincial Police confirmed the number of victims and said that 39 others escaped the scene without injury.
Trudeau called the attack "cowardly" in a tweet earlier in the night.
"Quebec is in shock tonight following the drama that occurred at the Center culturel Islamique de Québec," the mayor of Quebec City, Régis Labeaume, said in a statement. "My first thoughts go to the victims and their affected families as they gathered for prayer."
"Quebec City is an open city where everyone must be able to live together in safety and respect," the mayor added. "I invite all the people to unite and to be in solidarity. Québec is strong, Québec is proud, Québec is open to the world."
The New York Police Department said it would beef up patrols of mosque and other houses of worship within its city.
In a statement released on Sunday night, the NYPD said Critical Response Command personnel had been assigned to "extended tour coverage at certain mosque locations." It also said that it was monitoring the situation in Quebec.
NYC mayor Bill de Blasio took to Twitter to express his condolences and urged New Yorkers to "be vigilant."
"To my fellow New Yorkers who are Muslim: New York City will protect you. The NYPD will protect you. We will fight all hatred and bias," de Blasio said in a later tweet.
Quebec City Islamic Cultural Centre President Mohamed Yangui told the Associated Press the shooting occurred in the men's section of the mosque. He said he wasn’t present at the time of the attack, but he got details from witnesses who were on the scene.
"We are sad for the families," he told The AP.
This is a developing story. Check back for more details.
ABC News' Rachel Katz and The Associated Press contributed to this report.