Nearly 200 unmarked graves have been discovered near another school site in Canada, the third such find during the past one month.
Another 182 unmarked graves have been discovered at a Catholic Church-run school in Canada where children from indigenous communities were forcibly taken away from their families.
Experts used ground-penetrating radar to locate the remains of pupils aged seven to 15 at the former St Eugene's Mission School near Cranbrook, British Columbia, the Lower Kootenay Band said on Wednesday.
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.
The continuing discovery of such graves has become an embarrassment for Canadian leadership, which has taken pride in opening its borders to migrants from different countries.
Calls have grown on the Pope to apologise to survivors of the schools that were run by the Catholic Church on behalf of the federal government from 1912 until the early 1970s.
Some of the graves found at St Eugene's Mission School are as shallow as three to four feet (0.9 to 1.2 meters), the Band 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.
Prime Minister Justin Trudeau told a press conference 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."
Two churches went up in flames early on Wednesday 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.
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 vandalised, including with red paint.
'A Cultural genocide'
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.
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 apologised 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.
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 apologise 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 $20 million in compensation to former students.