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Prime Minister Justin Trudeau has pledged "full reconciliation" with Canada's indigenous peoples after a report detailed decades of abuse.

Speaking at the release of the Truth and Reconciliation Commission's final report on Tuesday, he said he wants the government to accept responsibility.

The report found a school system for indigenous children separated families and tried to weaken their culture.

Over 3,000 children died while at the schools over the last century.

Six years in the making, the nearly 4,000-page report found they died at a higher rate than the general population and many were buried in unmarked graves.

Former Prime Minister Stephen Harper apologised to survivors in 2008, but some critics saw the apology as hollow.

Mr Trudeau said the final report builds on Mr Harper's apology and "sets us squarely on a path to true reconciliation".

"Our goal, as we move forward together, is clear: it is to lift this burden from your shoulders, from those of your families and communities," said Mr Trudeau, speaking to survivors of the schools in Ottawa. "It is to accept fully our responsibilities and our failings, as a government and as survivors."

Government-led policy amounted to cultural genocide, the found.

The commission found the policy was enacted because the country "wished to divest itself of its legal and financial obligations to Aboriginal people and gain control over their land and resources."

From 1840 to 1996, more than 150,000 First Nations, Metis ands Inuit children were separated from their families and placed in the government-run schools, in an attempt to rid them of their "Indian" culture.

Many endured emotional, physical and sexual abuse, with the final report detailing cases of rape and malnutrition.

The schools were run by Christian churches. Many survivors are still recovering from having their families separated for decades.

Mr Trudeau has set up a government inquiry to investigate missing and murdered indigenous women.

He said last week the Canadian government must renew its relationship with indigenous peoples.

"It is my deepest hope that this report and its findings will help heal some of the pain...The Government of Canada sincerely apologises and asks forgiveness of the Aboriginal peoples of this country for failing them so profoundly," Mr Trudeau said.

"We have a plan to move towards a nation-to-nation relationship based on rights, respect, cooperation and partnership, and we are already making it happen."

He pledged that the government would enact all of the report's recommendations, beginning with the implementation of the United Nations Declaration on the Rights of Indigenous Peoples.

The government will also work with indigenous leaders on a "national reconciliation framework", he said.