Earlier, remains of 215 children in unmarked graves were found in British Columbia in May and 751 more unmarked graves were discovered in Saskatchewan last week.
Another 182 unmarked graves were discovered at a third former indigenous residential school in Canada as two Catholic Churches went up in flames on Wednesday, with anger mounting over the mushrooming abuse scandal.
The Lower Kootenay Band said experts using ground-penetrating radar mapping located what are believed to be the remains of pupils aged seven to 15 at the former St Eugene's Mission School near Cranbrook, British Columbia.
Some of the graves are as shallow as three to four feet (.9 to 1.2 meters), it said. They are believed to be the remains of members of bands of the Ktunaxa nation, which includes the Lower Kootenay, and neighboring indigenous communities.
The Catholic Church operated the school on behalf of the federal government from 1912 until the early 1970s.
The grim development follows the discovery of remains of 215 children in unmarked graves at the former Kamloops Indian Residential School in British Columbia in May and 751 more unmarked graves at another school in Marieval, Saskatchewan last week.
At a news conference, Prime Minister Justin Trudeau said these "horrific discoveries" have forced Canadians "to reflect on the historic and ongoing injustices that Indigenous peoples have faced."
He urged all to participate in reconciliation, while denouncing vandalism and arson of churches across the country.
"The destruction of places of worship is not acceptable, and it must stop," he said. "We must work together to right past wrongs. Everyone has a role to play."
In the early morning, two churches went up in flames amid growing calls for a papal apology over abuses at Canada's residential schools.
Police said the fires at the Morinville church north of Edmonton, Alberta and the St. Kateri Tekakwitha Church on Sipekne'katik First Nation near Halifax in Nova Scotia are being investigated as possible arson.
"We are investigating it as suspicious," Royal Canadian Mounted Police Corporal Sheldon Robb told AFP, speaking on the fire that gutted the Morinville church.
Corporal Chris Marshall of the Nova Scotia RCMP said the same about the fire that severely damaged the St. Kateri Tekakwitha Church.
The blazes brought to eight the number of churches across Canada destroyed or damaged by suspicious fires, most of them in indigenous communities, in recent days.
Several others were vandalized, including with red paint.
No direct link has officially been made between the church fires and the discovery of the unmarked graves.
But speculation is rampant, amid intense anger and sadness triggered by the burial finds.
"We absolutely recognize the profound effect the discoveries of the unmarked graves have had on First Nations people, and investigators will bear that in mind," Marshall said.
The damaged churches were built a century ago, coinciding with the opening of 139 boarding schools set up to assimilate indigenous peoples into the Canadian mainstream.
Until the 1990s, some 150,000 Indian, Inuit and Metis youngsters were forcibly enrolled in the schools, where students were physically and sexually abused by headmasters and teachers who stripped them of their culture and language.
More than 4,000 died of disease and neglect in the schools, according to a commission of inquiry that concluded Canada had committed "cultural genocide."
Trudeau last Friday apologized for the "harmful government policy" and joined a chorus of indigenous leaders' calls for Pope Francis to do the same for abuses at the schools.
The flag atop parliament has been lowered to commemorate the pupils' deaths, and will remain at half-mast for Canada's national day on July 1, he said Wednesday.
National Chief of the Assembly of First Nations Perry Bellegarde said "each of the (grave) sites need to be investigated properly." More searches of burial sites have been launched or are being planned.
He also renewed calls for the pope to apologize on Canadian soil directly to former students, referred to as residential school survivors in Canada.
Their experiences, he said, have caused "intergenerational trauma that is felt to this day."
He added that it was important that the pope "speak directly to the survivors here" in order to create "healing and reconciliation."
The Federation of Sovereign Indigenous Nations (FSIN), which represents 74 tribes in Saskatchewan, meanwhile noted that the church had yet to fulfill its promise to provide Can$25 million (US$20 million) in compensation to former students.
The church so far has raised and handed over a paltry Can$34,650, it said in a statement.
"For Catholics to raise millions to build multiple multi-million-dollar cathedrals and raise only $34,650 or $0.30 per survivor is shameful," the FSIN said a statement.