Canadian Prime Minister Justin Trudeau has condemned a wave of violence across Canada that has seen a number of churches attacked.

The attacks on the churches are believed to be in retaliation for the grim discovery of Indigenous children's remains at residential schools.

The residential schools were established in the 1800s to forcibly assimilate Indigenous people into Canadian society.

According to Canadian broadcaster CBC, over 150,000 First Nations, Métis and Inuit children were forced to attend the schools from the 1870s until 1997.

In May, the remains of 215 children were found buried in unmarked graves at the Kamloops Indian Residential School in British Columbia, which operated under the auspices of the Catholic Church from 1890 to 1969. In its final years, it was under the control of the federal government before finally closing in 1978.

A few weeks later in June, Cowessess First Nation said 751 unmarked graves had been discovered at the site of another former residential school in Saskatchewan.

Trudeau said the discoveries were "a shameful reminder of the systemic racism, discrimination, and injustice that Indigenous peoples have faced".

The Prime Minister, a Catholic, has also called on Pope Francis to issue a formal apology. The Canadian Conference of Catholic Bishops has said Pope Francis will meet Canadian Indigenous leaders later this year about an apology.

Canada Day on Thursday saw a number of churches vandalized and statues desecrated, with one of Queen Victoria and another of Queen Elizabeth II both toppled. 

A 108-year-old Anglican church in Gitwangak, a First Nation village near New Hazelton, in British Columbia, was completely destroyed by fire on Thursday night. 

On the same night, an Anglican church in Tofino, British Columbia, suffered minor damage in another suspicious fire.

Several Catholic churches have also suffered fires in recent weeks, prompting the federal government to pledge funding for security at churches.

Ten churches were reportedly desecrated in Alberta state on Canada Day.

Alberta's Premier Jason Kenney said they included an African Evangelical Church in Calgary whose congregation is formed entirely of refugees.

"These folks came to Canada with the hope that they could practise their faith peacefully," he tweeted.

"Some of them are traumatised by such attacks.

"This is where hatred based on collective guilt for historic injustices leads us. Let's seek unity, respect & reconciliation instead."

Speaking to reporters on Friday, Trudeau said he could understand the anger but added that acts of violence against churches were not the answer to the scandal.

"It is unacceptable and wrong that acts of vandalism and arson are being seen across the country, including against Catholic churches," he said.

"I can't help but think that burning down churches is actually depriving people who are in need of grieving and healing and mourning (of) places where they can actually grieve and reflect and look for support.

"We shouldn't be lashing out at buildings that can provide solace to some of our fellow citizens. But we should be, every day, committing ourselves, each and every one of us, to the hard work that we need to do to actually rebuild a path forward that reflects the terrible intergenerational trauma and present day realities of suffering that we are all collectively responsible for."