Chief Rosanne Casimir of the Tk'emlups te Secwépemc First Nation stated ground-penetrating radar was used to verify the find.
More bodies might be found because there were more areas to search on the school grounds, Ms Casimir said.
Earlier she predicted the discovery that an"unthinkable reduction which was talked about but never recorded in the Kamloops Indian Residential School".
A report over five decades ago with a Truth and Reconciliation Commission detailed harsh mistreatment inflicted on Native children in the associations.
It stated at least 3,200 kids had died amid neglect and abuse, and there were reports of 51 deaths at the Kamloops faculty alone between 1915 and 1963.
"This resurfaces the dilemma of residential schools and the consequences from this heritage of genocide towards Native people," Terry Teegee, Assembly of First Nations regional leader for British Columbia, said.
British Columbia Premier John Horgan said that he was"horrified and heartbroken" to learn of this discovery, calling it a tragedy of"unthinkable proportions" that emphasized the violence of their residential school program.
Ms Casimir said it was thought the deaths were but a neighborhood museum archivist was working with the Royal British Columbia Museum to see whether any records of these deaths could be found.
"Given the magnitude of this school, with up to 500 students registered and attending at any one time, we understand that this supported loss affects First Nations communities throughout British Columbia and outside," Ms Casimir said.
Ms Casimir said officials were telling community members who had children who attended the school.
The First Nations Health Authority called the discovery of their children's remains"extremely painful" and said in a website posting it might:"have a substantial impact on this Tk'emlúps community and also in the communities served by this residential college ."
The authority's CEO, Richard Jock, said the discovery illustrated"the harmful and lasting impacts the residential college system has been on First Nations people, their communities and families".
Nicole Schabus, a law professor at Thompson Rivers University, said all her first year law students in the Kamloops university spent at least one day at the former residential college talking with survivors about the conditions they endured.
She stated she did not hear survivors talk about an unmarked grave area,"but all of them talk about the children who didn't create it".