Pope Benedict has said he is sorry for the physical and sexual abuse and "deplorable" conduct at Catholic church-run Canadian residential schools.

The Vatican says the pontiff expressed his sorrow and emphasized that "acts of abuse cannot be tolerated" at a meeting Wednesday with representatives of native Canadians.

"Given the sufferings that some indigenous children experienced in the Canadian residential school system, the Holy Father expressed his sorrow at the anguish caused by the deplorable conduct of some members of the church and he offered his sympathy and prayerful solidarity," a statement from the Vatican said.

Archbishop Gerard Pettipas of the Canadian Conference of Catholic Bishops, who attended Wednesday's meeting, says it was an important moment.

Until today, the Church as a whole had never apologized for the abuse that aboriginal students suffered at the hands of Catholic missionary congregations.

"What we've been trying to do is to bring about healing and reconciliation between the Church, the government of Canada and our First Nations people," he told Canada AM shortly after the meeting.

"There was a feeling that despite the apologies that were offered by the oblates and some bishops, that the Catholic Church as a whole has not recognized the part that we played.

"As a gesture of reconciliation... it was important to hear from the one person who does speak for the Catholic Church around the world, to hear him say 'I am sorry. I feel for what you people have suffered. We hope that we can turn the page and move toward a better future together.'"

Chief Edward John of the Tlazten First Nations says he hopes the apology will help "many people move forward."

"We heard the prime minister's apology a year ago in June. And today, to listen to the Holy Father explain his profound sorrow and sadness and to express that there was no room for this sort of abuse to take place in the residential schools, that is an emotional barrier that now has been lifted for many people," he said.

Phil Fontaine, national chief of the Assembly of First Nations, said he appreciated the apology from the Church.

"I think His Holiness understands the pain that was endured by so many and I heard him say that it caused him great anguish," said Fontaine, who attended the meetings, on Wednesday.

"I also heard His Holiness say that the abuse of the nature that was inflicted on us has no place in the Church, it's intolerable and it caused him great anguish."

"What I heard," Fontaine added, "it gives me comfort."

More than 150,000 native children were forced to attend the schools from the 19th century until the 1970s. It was part of an effort to remove them from the influence of their homes and culture and assimilate the children into Canadian society.

The Canadian government has admitted that physical and sexual abuse in the schools was rampant. Many students recall being beaten for speaking their native languages and losing touch with their parents.

Prime Minister Stephen Harper issued a formal apology in Parliament last year, calling the treatment of children at the schools a sad chapter in the country's history. He said the policy of forced assimilation was wrong, caused great harm, and had no place in the country.

Canada has also offered compensation, as part of a lawsuit settlement between the government, churches and surviving students.