The pope called for Canada's political and religious leaders to work together to "shed light on this sad matter" and begin the process of "reconciliation and healing".
The pope also offered prayers "for the grief-stricken indigenous families and communities of Canada."
In comments on June 4, Trudeau stressed: "We need to have truth before we can talk about justice, healing and reconciliation."
UN rights experts on June 4 urged both Ottawa and the Vatican to hold swift and thorough investigations into the affair.
A Canadian truth and reconciliation commission has made dozens of recommendations -- including seeking a papal apology.
On June 2, Vancouver Archbishop J Michael Miller offered an apology on behalf of the Church in a statement.
But there have been growing calls for an apology from the pope himself -- including from some Canadian government ministers.
The Kamloops Indian Residential School was the largest of 139 boarding schools set up in the late 19th century to assimilate Canada's indigenous peoples, with up to 500 students registered and attending at any one time.
The boarding schools aimed at 'civilizing' pupils by instilling Western values
Only 50 deaths were ever officially recorded at the institution, where a principal once pleaded for more funds to properly feed students.
It was operated by the Catholic Church on behalf of the Canadian government from 1890 to 1969 before Ottawa took over its administration and closed it a decade later.
The boarding schools aimed at "civilizing" pupils by instilling Western values.
But survivors have alleged they were mistreated and abused by priests and nuns. They say their hair was cut, they were forbidden to speak their traditional language and perform their dances. They were also forced to cut ties with families.
An estimated 150,000 children were forced into the system. Many of them, separated from their families and given a European name, suffered physical and sexual abuse, while thousands disappeared, according to the results of an inquiry.