A grim report into Canada's residential school system should serve as a "wake-up call" to end the ignorance surrounding the dark period in the country's history, says the head of the Truth and Reconciliation Commission of Canada.

The research released Monday shows at least 3,000 children are now known to have died while in the Indian residential schools system that started in the 1870s. The new numbers are the result of the first systematic search of government, school and other records.

Marie Wilson, commissioner of the Truth and Reconciliation Commission, said the numbers are shocking. Of the 3,000 confirmed to have died, she said, 500 are children whose identities remain entirely unknown.

"I hope it's a huge wake-up call to Canada about the enormity of the impacts of the residential school story," she told CTV's Canada AM on Tuesday.

"We've heard about it in the global way, but now, to know these are real little lives that were lived and lost in the context of going to school is something we all need to pay attention to and we need to ask ourselves questions about what it means for today."

Alex Maass, research manager with the Missing Children Project, compiled the numbers after extensive research. Each death was confirmed through documentation showing when the child died, where the death occurred and what the circumstances were.

Disease was the largest killer, particularly tuberculosis which flourished in the crammed, dormitory-style accommodations. The Spanish flu was also devastating, and children are shown to have died from malnutrition or accidents such as fires, drowning or exposure. Others were the victims of physical and sexual abuse, while some died trying to run away and others committed suicide.

Alvin Dixon, a survivor of the residential school system in B.C. who now counsels other natives, said the report's description of overcrowding, physical abuse and disease is true to his experience.

"I was only there for about two hours when I got my first strapping for speaking (my) language," Dixon said. "I spoke very little English then, I was 10 years old, and the other impression I have is the overcrowding and the smell of little children, of too many people in one room."

About 150,000 First Nations children went through the church-run residential school system, which ran from the 1870s until the 1990s. The new records reveal the number of deaths only began to drop significantly after the 1950s, although some fatalities occurred as recently as the 1970s.

Maass said death was such an expected part of the residential school system that buildings were often designed with a cemetery as a key feature in the architectural plans.

He warned the death toll is likely to go up as more documents are uncovered.

Wilson said she hopes the new insights will allow all Canadians to learn from the past and avoid making similar mistakes in the future.

"We have remedial learning to do which is very significant because most of us grew up knowing nothing about residential schools. So our school systems, our departments of education have work to do to make this mandatory so we're not investing in another generation of ignorance," she said.