Religious freedom, the conflict in Ukraine and the environment were also on the table as Pope Francis met briefly with Harper, the Vatican said.
The Prime Minister's Office said their discussions included reference to the findings, released June 2, of the commission, which detailed the treatment of aboriginal children in residential schools supported by the Canadian government but administered by religious organizations, including the Catholic Church.
The commission described what happened to the children and their communities as "cultural genocide."
The national chief of the Assembly of First Nations had asked Harper to raise the issue with Pope Francis and to ask the Pope to publicly apologize for the Catholic Church's role in the schools, in the treatment of the children there and in its impact on the aboriginal cultures. Among the commission's recommendations was that the Pope come to Canada within a year and make a personal apology on behalf of the Catholic Church.
The Vatican's statement about the meeting did not mention the schools, which operated over a period of 130 years and separated some 150,000 native children from their families.
On other topics, "Prime Minister Harper was pleased to invite Pope Francis to Canada to celebrate Canada's 150th anniversary of Confederation" in 2017, his office said.
The prime minister was on a trip that included visits to Ukraine, Poland and Germany for the G7 summit of the leaders of the world's most industrialized countries.
Harper spent only about 10 minutes speaking privately with Pope Francis in the presence of interpreters, but after the prime minister introduced members of his entourage and posed for photographs with the Pope, the two continued talking. The prime minister also met with Archbishop Paul R. Gallagher, the Vatican equivalent of a foreign minister.
"During the course of the cordial discussions, the good relations existing between the Holy See and Canada were noted, as was the positive spirit of co-operation and dialogue between the Canadian federal government and the Church," said a Vatican statement.
The defense and promotion of religious freedom, tensions in Europe and the Middle East, the fight against terrorism and environmental issues were also discussed, the Vatican said.
According to the Prime Minister's Office, the reference to Europe was specifically about Ukraine and the ongoing fighting along its eastern border with Russia.
"Prime Minister Harper addressed the situation in Ukraine and his deep concern with Vladimir Putin's aggression, occupation and violence in Ukraine," his office said.
Harper has been a vocal critic of Putin over Russian aggression in Ukraine.
The previous day, Pope Francis had met with Putin for 50 minutes and emphasized the importance of rebuilding a climate of dialogue, Vatican spokesman Federico Lombardi told journalists. The Pope also talked about the grave humanitarian situation in the country and the need to give access to relief workers, Lombardi said.
The Vatican did not say whether Francis challenged Russia on its role in the Ukraine conflict.