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.
The children were students at the Kamloops Indian Residential School in British Columbia that closed in 1978.
The discovery was announced recently 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 the city of Kamloops, said the preliminary finding represented an unthinkable loss that was never documented by the school's administrators.