The children were students at the Kamloops Indian Residential School in British Columbia that closed in 1978.
The discovery was announced on Thursday by the chief of the Tk’emlups te Secwepemc First Nation.
Prime Minister Justin Trudeau said it was a “painful reminder” of a “shameful chapter of our country’s history”.
The First Nation is working with museum specialists and the coroner’s office to establish the causes and timings of the deaths, which are not currently known.
Rosanne Casimir, the chief of the community in British Columbia’s city of Kamloops, said the preliminary finding represented an unthinkable loss that was never documented by the school’s administrators.
Canada’s residential schools were compulsory boarding schools run by the government and religious authorities during the 19th and 20th Centuries with the aim of forcibly assimilating indigenous youth.
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The schools that had cemeteries instead of playgrounds
Kamloops Indian Residential School was the largest in the residential system. Opened under Roman Catholic administration in 1890, the school had as many as 500 students when enrollment peaked in the 1950s.
The central government took over administration of the school in 1969, operating it as a residence for local students until 1978, when it was closed.The Tk’emlups te Secwepemc First Nation said the remains were found with the help of a ground-penetrating radar during a survey of the school.
“To our knowledge, these missing children are undocumented deaths,” Ms Casimir said. “Some were as young as three years old.”
“We sought out a way to confirm that knowing out of deepest respect and love for those lost children and their families, understanding that Tk’emlups te Secwepemc is the final resting place of these children.” The tribe said it had reached out to the home communities whose children attended the school. They expected to have preliminary findings by mid-June. British Columbia’s chief coroner Lisa Lapointe told Canadian broadcaster CBC “we are early in the process of gathering information”.