About 150,000 children spent months or years isolated from their families, language and culture, and many were physically and sexually abused by headmasters and teachers.
Pope Francis has issued a historic apology to Canadian indigenous peoples for the Roman Catholic Church's role in residential schools that sought to erase their cultures and where many children suffered abuse and were buried in unmarked graves.
Francis, in an address to native leaders after meetings with delegates from various indigenous nations on Friday, also said he hoped to visit Canada in July.
One of the leaders, who want the pope to make the apology directly to their communities on their native lands in Canada, called his words "historic" and another said they reflected the "entirety" of their message to him.
"For the deplorable behaviour of those members of the Catholic Church, I ask forgiveness from God and I would like to tell you from the bottom of my heart that I am very pained," he said, speaking in Italian.
"I join my brother Canadian bishops in apologising," he said. His speech in the Vatican's frescoed Sala Clementina was preceded by prayers by indigenous leader in native languages asking the "great spirit" to bless all those present.
"The pope's words today were historic to be sure. They were necessary and I appreciate them deeply," said Cassidy Caron, president of the Métis National Council and the head of one indigenous delegations.
"I now look forward to the pope's visit to Canada."
About 150,000 children were taken from their homes. Many were subjected to abuse, rape and malnutrition in what the Truth and Reconciliation Commission in 2015 called "cultural genocide".
The stated aim of the schools, which operated between 1831 and 1996, was to assimilate indigenous children. They were run by Christian denominations on behalf of the government, most by the Catholic Church.
READ MORE: Explained: Canada’s 'cultural genocide' of Indigenous people
Sorrow and shame
"I feel shame – sorrow and shame – for the role that a number of Catholics, particularly those with educational responsibilities, had in all these things that wounded you, in the abuses you suffered and in the lack of respect shown for your identity, your culture and even your spiritual values," Francis said.
Francis, who also spoke of "unresolved traumas that have become intergenerational traumas," told the indigenous peoples that he was happy to know that Catholics among them were devoted to St. Anne, the mother of Mary. The feast of St. Anne is July 26.
"This year, I would like to be with you on that day," he said.
"I won’t come in the winter!" he joked with them, drawing laughs.
READ MORE: Mass grave of Indigenous children found in Canada, Trudeau pledges 'action'
The scandal erupted anew last year with the discovery of the remains of 215 children at the former Indian Residential School in Kamloops in the Western Canadian province of British Columbia, which closed in 1978.
The find brought fresh demands for accountability. Hundreds more unmarked burial sites have been identified since.
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