The investigation, initiated by the US Secretary of the Interior, shows that at least 973 children died as a result of abuse, diseases, and harsh treatment in the US federal boarding school system over a 150-year period.
The boarding schools' operations, which were reviewed in the government investigation, continued until 1969.
The investigators have found both marked and unmarked graves at 65 of the more than 400 boarding schools established to assimilate Native American children into the dominant society's norms.
The graves do not specify the cause of death, but the investigation's officials say it involved abuse, diseases, and accidents.
The investigation, presented on Tuesday, was initiated after numerous former students from the US indigenous population told of the harsh treatment they endured when they were separated from their parents and forced into boarding schools.
In a preliminary report from 2022, it was estimated that over 500 children had died during their schooling at boarding schools.
"The federal government took deliberate and strategic actions through federal Native American boarding schools to isolate children from their families, deny them their identities and their language, culture, and contacts that are fundamental to indigenous peoples," wrote US Secretary of the Interior Deb Haaland in connection with the report's publication.
Haaland is the first minister in a US government to come from one of America's indigenous peoples.