In 2008, former prime minister Stephen Harper issued an apology on behalf of Canadians, calling it "a sad chapter in our history".
Trudeau, a Catholic who was educated at a Jesuit school and a fervent backer of gay rights, later said that he told the pontiff "about how important it is for Canadians to move forward on a real reconciliation with the indigenous people".
Canada's Truth and Reconciliation Commission's Calls to Action aims to redress the legacy of residential schools and advance the process of Canadian reconciliation.
Some 150,000 aboriginal children were forcibly removed from their families, and sent to live in church-run boarding schools where they were forbidden to speak their language or practise their own culture.
Pope Benedict formally apologized in 2009 for the Church's complicity in residential schools in a meeting with Phil Fontaine, then National Chief of the Assembly of First Nations, and other Native leaders, who met with the Pope in the Vatican.
"He reminded me his entire life has been dedicated to supporting marginalized people in the world and fighting for them and he looked forward to working with me and the Canadian bishops to figure out a path forward together".
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The Vatican said the conversation "focused on the themes of integration and reconciliation, as well as religious freedom and current ethical issues" but did not mention an apology directly.
"T$3 he good bilateral relations between the Holy See and Canada were evoked, along with the contribution of the Catholic Church to the social life of the country".
Trudeau told reporters he invited the Pope to go to Canada "in the coming years", but added no further details about such a trip.
It is unusual for a government or head of state to "pre-brief" what they are going to say to the Pope: papal audiences, and what is discussed, normally remain private. The Prime Minister's Office called it a 42-minute meeting.
In return, the Pope gave the prime minister a gold medal marking the fourth year of his pontificate, an autographed copy of his message for World Peace Day and three papal letters about family, the environment and evangelism.
Trudeau met with The Pope at the Vatican on Sunday where they discussed reconciliation efforts between the Catholic Church and groups marginalized by Canada's residential schools.
On Tuesday, Trudeau will continue his official visit to Italy, where he will meet Prime Minister Paolo Gentiloni and deliver an address to parliamentarians. "So this follow with Prime Minister Trudeau today is really great news", Mr. Littlechild said.