“Aboriginal people, on the other hand, see reconciliation as an opportunity to affirm their own sovereignty and return to the ‘partnership’ ambitions they held,” the report said.

Prime Minister Stephen Harper’s Conservative government has had a strained relationship with indigenous people, even though it was Mr. Harper who made the apology in 2008. When a reporter at a news conference on Tuesday asked whether the Conservatives were at all likely to adopt the commission’s recommendations, Justice Sinclair said, “We are writing for the future, not just for this government,” a remark that met with prolonged applause and cheers from the largely aboriginal audience.

Bernard Valcourt, the aboriginal affairs minister, said Tuesday: “This dark chapter in Canada’s history has left a mark on our country. I’m confident that we can build on the important work that’s been done and continue to heal as a nation.”

Leaders of the Protestant churches that ran many of the schools apologized long ago. But the report and Justice Sinclair urged Pope Francis to formally take that step for the Roman Catholic Church, which ran some of the schools, saying that apologies from local Catholic officials were not enough.

The research and interviews conducted by the commission detailed a boarding school system that was woefully underfunded, inadequately staffed and largely ineffective at its stated aim of providing useful education.

Some former students interviewed by the commission cited school sports and music and arts programs as bright spots in their lives. But those programs were not generally part of the system, and most former students, even those who were not physically or sexually harmed or neglected, said their daily lives had been heavily regimented and lacked privacy and dignity. At many of the schools, students were addressed and referred to by number as if they were prisoners.

“In the school, I didn’t have a name,” Lydia Ross, a former student, told the commission. “I had No. 51, No. 44, No. 32, No. 16, No. 11 and then finally No. 1, when I was just coming to high school.”