Canadian Muslims expressed fear on Sunday that a backlash had begun.
The vandals struck overnight at the west-end mosque, a police official said on Sunday. A second official said he had no information on any link between the incident and the arrests, which began late on Friday.
Bill Blair, Toronto police chief, told a meeting with Islamic community leaders: "It is certainly possible that that damage was motivated by hate. Hatred in any form, and certainly in its expressions of violence and damaged property, will not be tolerated in our community."
Mohammad Alam, president of the Islamic Foundation of Toronto, said the vandalism may be the beginning of religiously motivated reprisals against the country's Muslim population, estimated at more than 600,000.
He said he backed the government's efforts to combat terrorism, but emphasised nothing had been proven in the suspected bomb plot, which has gripped the country.
"Like everybody knows, this is so far all allegation," Alam said. "To us, it doesn't matter what religion they belong to - if they are a terrorist, they are a terrorist, they should be punished according to the law."
The west-end mosque in Toronto
that was damaged overnight
The arrested men, all Canadian residents or citizens, were charged with terrorism-related offences and made a brief court appearance on Saturday.
The 12 adults were sent to a high-security prison outside Toronto while the five youths were dispatched to area jails.
Police say the arrested men had amassed enough explosives to build a bomb larger than that used in 1995 against the federal building in Oklahoma City, USA, which killed 168 people, and they were planning to blow up targets in Ontario, Canada's political and economic heart.
The suspects, all from Ontario, remained in custody and their next court appearance is scheduled for Tuesday.
Acting Sergeant Michele Paradis of the Royal Canadian Mounted Police said that police do not anticipate more arrests, but "reams" of evidence still must be analysed.