The children were students at the Kamloops Indian Residential School in British Columbia, which 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.
