"These are actual confirmed numbers," Alex Maass, research manager with the Missing Children Project, told The Canadian Press from Vancouver.
“All of them have primary documentation that indicates that there’s been a death, when it occurred, what the circumstances were.”
But the unpublished research is raising questions.
In all, about 150,000 First Nations children went through the church-run residential school system, which ran from the 1870s until the 1990s.
"To evaluate numbers like this, you really should know what was the mortality rate of native American children in these years and what was the mortality rate of kids who were not in the schools versus kids who were in the schools," said Tom Flanagan, political science professor at the University of Calgary.
He added that the majority of First Nations children did not attend residential schools.
"To just suddenly hear 3,000 sounds terrible and it is terrible, but to put it into any kind of historical perspective there's a lot more information that you need to have," said Flanagan.
The largest single killer, by far, was disease.
Natives of both North and South America had no natural resistance to European diseases. Wave after wave of disease decimated the populations of native America and continued into the 20th century, he said.
"Mumps, measles, small pox, whooping cough, diphtheria, influenza - these were serious diseases for Europeans but they were lethal for the populations of the new world," said Flanagan.
"It was seriously thought that in the 19th century that Canadian Indians might disappear all together, they were sometimes referred to as the vanishing race," said Flanagan.
"The schools were a particular breeding ground for (TB)," Maass said. "Dormitories were incubation wards."
Flanagan said the deaths from disease in residential schools cannot be denied, but he added that situations could have been worse in isolated communities.
While a statistical analysis has yet to be done, the records examined over the past few years also show children also died of malnutrition or accidents. Schools consistently burned down, killing students and staff. Drowning or exposure was another cause.
Many students were physically, mentally and sexually abused. Some committed suicide. Some died fleeing their schools.