The Catholic church that ran the Marieval Indian Residential School about 87 miles (140 km) from the provincial capital Regina, removed the headstones, Cowessess First Nation Chief Cadmus Delorme told reporters.
It is not clear how many of the remains detected belong to children, Delorme said. "There are oral stories that there are adults in this gravesite as well."
According to Canada's Truth and Reconciliation Commission, which published a report that found the country's residential school system amounted to cultural genocide, a cemetery was left on the Marieval site after the school building was demolished.
"We are not asking for pity. We are asking for understanding," Delorme said.
"We didn't remove the headstones. Removing headstones is a crime in this country. We are treating this like a crime scene," he added.
The Cowessess First Nation began a ground-penetrating radar search on June 2, after the discovery of 215 unmarked graves at the Kamloops Residential School in British Columbia.
The Kamloops discovery reopened old wounds in Canada about the lack of information and accountability around the residential school system, which forcibly separated indigenous children from their families.