A crowd chanted “no pride in genocide” before pulling down the statues of the monarchs.
The action took place on Canada Day on Thursday, when traditionally celebrations take place across the country.
However, many cities scrapped events this year as the scandal over the indigenous children made Canadians confront their colonial history. Prime Minister Justin Trudeau said the day would be “a time for reflection”.
Almost 1,000 unmarked graves have been found at former residential schools in British Columbia and Saskatchewan that were mainly run by the Catholic Church and funded by the government.
For 165 years and as recently as 1996, the schools forcibly separated indigenous children from their families, subjecting them to malnourishment and physical and sexual abuse in what the Truth and Reconciliation Commission called “cultural genocide” in 2015.
In Winnipeg, a crowd cheered as Queen Victoria’s statue fell outside the Manitoba provincial legislature. Protesters, many of whom wore orange clothing, also kicked the toppled statue and danced around it. The pedestal and statue were daubed in red paint hand marks.
A nearby statue of Queen Elizabeth was also pulled down. She is Canada’s current head of state, while Victoria reigned from 1837 to 1901 when Canada was part of the British Empire.
Protests in support of the indigenous children also took place on Thursday in Toronto, Canada’s financial hub, while a #CancelCanadaDay march in the capital Ottawa drew thousands in support of victims and survivors of the residential school system.
Vigils and rallies were held across other parts of the country. Many participants wore orange clothing, which has become the symbol of the movement.
In his Canada Day message, Trudeau said the discoveries of the remains of the children at the former schools “have rightfully pressed us to reflect on our country’s historical failures”. Injustices still exist for indigenous peoples and many others in Canada, he said.
(Reporting by Kanishka Singh in Bengaluru; Editing by Angus MacSwan)