Over a breakfast with journalists on Monday, Archbishop Richard Smith said he has advised the pope to consider Prime Minister Justin Trudeau's request for the Vatican to issue a formal apology to Canada's Indigenous peoples.
"I told him about how important it is for Canadians that we move forward on real reconciliation with Indigenous peoples and highlighted how he could help by issuing an apology", Trudeau told reporters following the 42-minute long meeting.
The commission made 94 recommendations, including that the pope issue a formal apology in Canada to survivors and their descendents for the Church's "role in the spiritual, cultural, emotional, physical, and sexual abuse" of the children. The TRC report said the church-run schools attempted to assimilate Indigenous children by removing their culture, identity and language.
Trudeau said that in their private talks, the pope "reminded me that his entire life has been dedicated to supporting marginalized people in the world, fighting for them, and that he looks forward to working with me and with the Canadian bishops to figure out a path forward together".
The meeting focused on "the themes of integration and reconciliation, as well as religious freedom and current ethical issues", the Vatican said in a statement.
"In the cordial discussions the 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", read a statement from the Vatican.
The meeting was not Trudeau's first visit to the Vatican.
In 2009, former pope Benedict did express "sorrow" on behalf of the Catholic Church for the "deplorable conduct" by some members in their treatment of indigenous children in residential schools.
Trudeau also invited Pope Francis to visit Canada sometime in the near future.
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.
In 2015, Mr Harper met Pope Francis and called attention to the commission's findings.
The Pope in return gifted Trudeau a gold medal marking the fourth year of his pontificate, an autographed copy of his message for World Peace Day and three papal letters on the family, the environment and evangelism.
Trudeau, who is Catholic, says he gave the Pope a set of rare Jesuit Relations books, as well as a Montagnais-French dictionary penned by a 17th-century French Jesuit.
Trudeau said he and the pope also discussed climate change.