But he did not go so far as to offer the apology that many people have been calling for over the unfolding scandal.
“I follow with pain the news coming from Canada about the shocking discovery of the remains of 215 children,” he said, following Sunday prayers at Saint Peter’s Square.
The discovery of the remains of the children last month sent shockwaves through Canadian society.
Prime Minister Justin Trudeau on Friday called on the Catholic Church to take responsibility for its role in the deaths at the Kamloops Indian Residential School in British Columbia.
He has already promised “concrete action” from the government and urged his fellow Catholics in Canada to make it clear to the Church that they expected its full cooperation too.
“Before we have to start taking the Catholic Church to court, I am very hopeful that religious leaders will understand that this is something they need to participate in,” he added.
In his speech Sunday, Pope Francis said: “I unite with the Canadian bishops and the entire Catholic Church in Canada in expressing my solidarity with the Canadian people traumatised by this shocking news.
“The sad discovery further increases awareness of the pain and suffering of the past,” he added.
‘Reconciliation and healing’
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”.
But in his comments Friday, Trudeau stressed: “We need to have truth before we can talk about justice, healing and reconciliation.”
UN rights experts on Friday urged both Ottawa and the Vatican to hold swift and thorough investigations into the affair.
On Wednesday, 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.
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.