Shots were fired at the Quebec Islamic Cultural Centre on Sunday night, where more than 50 people had gathered for evening prayers.
One suspect was arrested at the scene and another was arrested nearby. Police do not believe there are other suspects at large.
The Canadian authorities are treating the shooting as a terror attack.
“We condemn this terrorist attack on Muslims in a centre of worship and refuge,” Prime Minister Justin Trudeau said in a statement.
“Muslim-Canadians are an important part of our national fabric, and these senseless acts have no place in our communities, cities and country.”
The president of the mosque, Mohamed Yangui – who was not inside at the time – said the shooting had happened in the men’s section of the mosque.
“Why is this happening here? This is barbaric,” he said.