Officials told Daniel Ten Oever's parents, Dan Ten Oever and mother Stephanie Huck, that the boy threw the chairs in St. Jerome Catholic School on Thursday.
A female Ottawa police officer then responded and put handcuffs on Daniel to restrain him, the parents told CBC News.
"I've lost faith in the Catholic school board and St. Jerome school. We're not putting our son back in school," Dan Ten Oever said.
"We're probably going to, most likely, going to change him into the public school board. We're really sad because this is our son and we're trying to protect him."
Ten Oever said he trusts his son because the boy does not understand how to lie, due to his autism. There is a disconnect, though, between his son's version of the story and the school board's.
Police, school board refuse comment on incident
The board told the parents that police used handcuffs on their own volition, while the boy told his parents the principal asked police to put Ten Oever in handcuffs.
Neither the Ottawa Catholic school board nor police would comment on the incident specifically, but school Supt. Mary Donaghy said the staff "acted appropriately to ensure the safety of everyone involved."
Police confirmed they responded to St. Jerome school and no charges were laid.
Spokesman Marc Soucy said police handcuff anyone deemed by an officer to be violent or a danger to themselves, others or the police. Neither the age nor size of a person changes that policy, he said.
Police would investigate if a complaint is launched against the officer, Soucy added.