At least 6,000 aboriginal children died while in the residential school system, says Justice Murray Sinclair, the chair of the Truth and Reconciliation Commission.

Sinclair, who has been tasked with studying the legacy of the residential schools, says that the figure is just an estimate and is likely much higher. Residential schools were established in the 19th century and the last ones closed in 1996.

"We think that we have not uncovered anywhere near what the total would be because the record keeping around that question was very poor," Sinclair told Rosemary Barton of CBC's Power & Politics. "You would have thought they would have concentrated more on keeping track."

Sinclair offered the figure of 6,000 in a later interview with Evan Solomon to air Saturday on CBC Radio's The House — much higher than earlier estimates that put the number of school children who died in the system at less than 4,000, but still possibly far short of the real outcome.

Sinclair, who was Manitoba's first aboriginal judge, said one estimate made in the early part of the 20th century was that 24 to 42 per cent of aboriginal children who attended the residential schools died at school or shortly after leaving school.

Most of the children died from malnourishment or disease. Some children who attended the schools in the 1940s and 1950s were even subjected to science experiments in which they were deprived essential nutrients and dental care.

The Truth and Reconciliation Commission, struck in 2009, is writing an exhaustive history of the residential school system. The commissioners interviewed over 7,000 people, and the final report, which is expected to be released on June 2, will span six volumes and include over two million words.

The new death toll comes in the wake of comments made by Beverley McLachlin, the chief justice of the Supreme Court. At an event on Thursday, McLachlin said that Canada attempted to commit "cultural genocide" against aboriginal peoples.

"The most glaring blemish on the Canadian historic record relates to our treatment of the First Nations that lived here at the time of colonization," McLachlin said. She was delivering the fourth annual Pluralism Lecture of the Global Centre for Pluralism, founded in 2006 by the Aga Khan, spiritual leader of Ismaili Muslims, and the federal government.

Canada, she said, developed an "ethos of exclusion and cultural annihilation."

Sinclair said he agrees with McLachlin's characterization of the country's history.

"I think as commissioners we have concluded that cultural genocide is probably the best description of what went on here. But more importantly, if anybody tried to do this today, they would easily be subject to prosecution under the genocide convention," Sinclair told Evan Solomon of CBC Radio's The House.

"The evidence is mounting that the government did try to eliminate the culture and language of indigenous people for well over a hundred years. And they did it by forcibly removing children from their families and placing them within institutions that were cultural indoctrination centres.

"That appears to us to fall within the definition of genocide under the UN convention," Sinclair said.

The United Nations' convention on the prevention and punishment of the crime of genocide does not address "cultural genocide," but it says genocide may include causing "mental harm" to a racial or religious group.

A spokesperson for Bernard Valcourt, the minister of aboriginal affairs, would not comment on the chief justice's remarks, but issued a statement saying, "While we cannot undo the past, we can learn from it and we have taken the steps necessary to bring closure to the legacy of the Indian residential schools."

In the 19th century, the Canadian government developed a policy of "aggressive assimilation" calling for aboriginal children to be taught at church-run, government-funded residential schools.

The government felt children were easier to mould than adults, and the concept of a boarding school was the best way to prepare them for life in mainstream society.

Canada's first prime minister, Sir John A. Macdonald, was a strong proponent of the system.

"When the school is on the reserve, the child lives with his parents who are savages; he is surrounded by savages, and though he may learn to read and write, his habits and training and mode of thought are Indian. He is simply a savage who can read and write," he told the House of Commons in 1883.

The last residential schools, St. Michael's Indian Residential School and Gordon Indian Residential School, both located in Saskatchewan, closed in 1996.

In 2008, Prime Minister Harper made a historic apology for the harm caused by the residential school system.