Alexandre Bissonnette, who made a brief court appearance after surrendering to authorities, was charged with six counts of premeditated murder and five of attempted murder, police said.
More indictments are expected later, police added.
"There are search warrants underway," a spokeswoman for the Royal Canadian Mounted Police told a press conference.
"We hope to obtain the evidence to reach the point where we will be able to lay terrorism and national security charges," she said.
So far, authorities have shed no light on what may have prompted the attack.
Local media said Bissonnette is a Quebec nationalist and anti-feminist who recently "liked" US President Donald Trump's page on Facebook. He also has reportedly expressed support for French far-right politician Marine Le Pen.
Both police and witnesses had initially described two masked men opening fire inside the mosque, where worshippers were gathered for evening prayer.
But authorities said Monday that a second person detained had only been questioned as a witness.
Explaining how one suspect was eventually let go, the RCMP said: "This morning and last evening we had reason to believe that two individuals should be arrested, that two people had participated."
After investigating, they said: "we reached the conclusion that we should focus on one single suspect. And there was no reason to believe that the other individual had participated."
-AFPÂ
