The Prime Minister's spokesman, Cameron Ahmad, said Trudeau's main agenda for the conversation with Francis was reiterating the open invitation to the Pope to come to Canada and for "reconciliation" with the indigenous communities on this point.
Canadian Prime Minister Justin Trudeau said he asked Pope Francis to help Canadians "move forward on a real reconciliation" with the country's indigenous people "by issuing an apology" on behalf of the Catholic Church for its role in harming their communities.
The Canadian government issued its own official apology in 2008.
Among their promises were an inquiry into why so many aboriginal women are murdered or go missing, and to enact the 94 calls to action of the Truth and Reconciliation Commission (TRC) on residential schools. Children robbed of their identity, and banned from speaking their native language or taking part in their culture.
Papal apologies are not uncommon, with John Paul II issuing a number throughout his papacy including a sweeping, all-encompassing apology for 2,000 years of sins made in St Peter's Basilica in 2000.
On Monday, Trudeau said he invited the Pope to visit Canada in the coming years, and thanked him for the global leadership he has shown on climate change.
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While in Italy, he also visited the Roma Soccer Club Stadium and will meet Italy's prime minister and president. Trudeau invited the pontiff to Canada, where he is expected to make the apology. The Prime Minister's Office described the audience as having been 42 minutes long.
"We talked about how important it is to both highlight the scientific basis of protecting our planet, with the moral and ethical obligation to lead and to build a better future for all people on this earth", he said.
U.S. President Donald Trump, who like Trudeau had been in Brussels for the North Atlantic Treaty Organisation leaders' meeting and in Sicily for the G7 summit, met the Pope for about 30 minutes last week.
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 Pope gave Trudeau the gold medallion minted for the fourth year of his pontificate (2016-17), which features an "embrace" as "a symbol of forgiveness, joy and mutual acceptance", according to the Vatican's description.
A Canadian truth and reconciliation commission wanted an apology from the Roman Catholic Church in its extensive list of recommendations in a 2015 report. "So this follow with Prime Minister Trudeau today is really great news", Mr. Littlechild said.