Six people were killed and eight wounded when gunmen opened fire at a Quebec City mosque during Sunday night prayers, in what Canadian Prime Minister Justin Trudeau called a "terrorist attack on Muslims".

Police said two suspects had been arrested, but gave no details about them or what prompted the attack.

Prime Minister Justin Trudeau said in a statement: "We condemn this terrorist attack on Muslims in a center of worship and refuge".

"Muslim-Canadians are an important part of our national fabric, and these senseless acts have no place in our communities, cities and country."

Initially, the mosque president said five people were killed and a witness said up to three gunmen had fired on about 40 people inside the Quebec City Islamic Cultural Centre. Police said only two people were involved in the attack.

The mosque's president, Mohamed Yangui, who was not inside when the shooting occurred, said he got frantic calls from people at evening prayers.

"Why is this happening here? This is barbaric," he said.

The shooting came on the weekend that Trudeau said Canada would welcome refugees, after US President Donald Trump suspended the US refugee program and temporarily barred citizens from seven Muslim-majority countries from entering the US on national security grounds.

The premier of Quebec province, Philippe Couillard, said security would be increased at mosques in Quebec City and Montreal.

"We are with you. You are home," Couillard said, directing his comments at the province's Muslim community.

"You are welcome in your home. We are all Quebecers. We must continue together to build an open welcoming and peaceful society".