Around 150,000 indigenous children of the Métis and Inuit tribes were interned within residential schools across Canada from the late 1800s to the 1990s.
The 2015 truth and reconciliation commission would later reveal they were the subject of horrific abuse and a concerted effort to divorce them from language culture and their whānau.
Last year, 1300 unmarked graves of students were found at several of the former schools and investigations continue with the expectation that many more will be discovered.
Francis delivered the speech from Rome, however, said he hoped to visit Canada in July.
Canadian Prime Minister Justin Trudeau called the apology a "step forward" but he and tribal leaders said they looked forward to receiving it in person.
"Canada's history will forever be stained by the tragic reality of the residential school system," Trudeau said.
"As a country, we must never forget the unthinkable tragedies that took place and we must honour the children who went missing and never came home."
Fourteen per cent of Aotearoa's Catholic diocesan clergy have been accused of abuse (including physical, emotional, sexual abuse or neglect) since 1950.
Several high-profile cases are linked to Catholic schools.
A Royal Commission into abuse in care in Aotearoa is ongoing, with speculation around a quarter of a million tamariki were abused in a state or faith-based care.
Speaking on behalf of Church leaders, Cardinal John Dew, Archbishop of Wellington and President of the NZ Catholic Bishops Conference apologised at the hearing last year.
The pope is yet to directly apologise for abuses in Aotearoa.
