Gunmen fired on about 40 people inside the Quebec City Islamic Cultural Center on Sunday at 8pm local time (01:00 GMT).
Police said two suspects had been arrested.
The mosque's president, Mohamed Yangui, was not inside the mosque at the time of the shooting. He received frantic calls from worshippers.
He said: "Why is this happening here? This is barbaric."
Speaking to Al Jazeera by phone, he said: "One of the administrators called me and said there was a shooting at the mosque. I am still in shock. I ran to the mosque ... I was told that one attacker was arrested at the scene while another one was arrested nearby."
'A terrorist attack on Muslims'
Canadian Prime Minister Justin Trudeau condemned the shooting as a "terrorist attack on Muslims in a centre of worship and refuge".
Philippe Couillard, premier of Quebec, said on Twitter that the attack "is a terrorist act", and called for "solidarity with Quebecers of the Muslim faith".
The mosque leader Yangui added that the mosque had not received any threats immediately before the attack.
"The neighbourhood is very peaceful. We have a good relationship with the government, the mayor of Quebec. We have no problem whatsoever," he said.
The mosque was previously targeted in an Islamophobic attack, however. In June 2016 during Ramadan, a pig's head was left on the mosque's doorstep along with a note that said "bon appetit". Pork is forbidden in Islam.
Basem Boshra, managing editor of the Montreal Gazette, told Al Jazeera that the centre is the city's biggest mosque of six, with some 5,000 members.
"There's a pretty strong Muslim community in Quebec City," he said, adding that there were plans to lower flags at the national assembly as a mark of respect for the victims
Canada's public safety minister, Ralph Goodale, said on Twitter that he was "deeply saddened" by the loss of life and injuries.
Greg Fergus, an MP in Quebec, described on Twitter the attack as "a terrorist act - the result of years of demonizing Muslims".
The attack comes amid widespread protests across the US in defiance of an executive order signed by President Donald Trump that bans immigrants and refugees from seven Muslim-majority countries.