Muslims make up about 2% of Canada’s population
At least 28 windows were broken but nobody appears to have been hurt in the overnight attack and a mosque official said five cars were also damaged.
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Police have not officially linked the attack on the mosque with the arrests.
But a spokesman assured Muslim community leaders that hate crimes would not be tolerated.
“It is certainly possible that that damage was motivated by hate,” Toronto Police Chief Bill Blair said.
“Hatred in any form, and certainly in its expressions of violence and damaged property, will not be tolerated in our community.”
Ameer Ali, secretary of the International Muslims Organization of Toronto which houses the mosque, said it was one of the largest in North America and has about 500 worshippers daily.
Senior Muslim community leaders also told The Associated Press they had been receiving threatening e-mails since the arrests were announced.
Twelve men were charged on Saturday with planning a bombing campaign in and around Toronto.
Canada’s intelligence agency said it had been inspired by al-Qaeda.
Five youths were also charged, following an investigation involving more than 400 officers.
Police seized bomb-making materials in a series of raids in Toronto, including three tons of ammonium nitrate.
Officials said the group, most of whose members appear to be Canadian residents from Muslim backgrounds, “posed a real and serious threat”.