Prime Minister Justin Trudeau on Friday denounced a wave of vandalism across Canada that saw churches damaged and statues of monarchs splashed with red paint and torn down.

These acts followed the recent discoveries of more than 1,000 unmarked graves at former indigenous boarding schools that has provoked anger and grief in indigenous communities, and beyond, along with a reckoning of the country's colonial history.

"It is unacceptable and wrong that acts of vandalism and arson are being seen across the country, including against Catholic churches," Trudeau told a news conference.

"I understand the anger that's out there, against the federal government, against institutions like the Catholic Church," he said.

"It is real, and it is fully understandable given the shameful history" of Canada's indigenous residential schools, he said.

But instead of wreaking destruction, he urged all Canadians to commit to reconciliation.

Canada's national holiday on Thursday was marked by a grim reckoning over its British colonial past, with several cities cancelling their usual Canada Day celebrations.

Ten churches in Calgary were also vandalised, and in Winnipeg protestors pulled a statue of Queen Victoria off its base at the Manitoba legislature, and another nearby of Queen Elizabeth II.

In Britain, a 10 Downing Street statement said London condemned the toppling of the statues of the two queens.

"Our thoughts are with Canada's indigenous community following these tragic discoveries (of graves) and we follow these issues closely and continue to engage with the government of Canada with indigenous matters," the official added.

Until the 1990s, some 150,000 Indian, Inuit and Metis youngsters were forcibly enrolled in 139 residential schools run by the Catholic church on behalf of the government.

More than 4,000 students died of disease and neglect.

Others have recounted physical and sexual abuses by headmasters and teachers who stripped them of their culture and language.

The 1904 statue of Queen Victoria, who reigned over this Commonwealth nation when Canada began negotiating treaties with First Nations and opened the first residential schools, was left covered with a Canadian flag with the words in black marker, "We were children."

Belinda Vandenbroeck, a former residential school student, told the Winnipeg Free Press: "This queen is the one that gave our land away just like that to her merry gentlemen -- her fur traders."

"So I really have no place for her in my heart," she said.