According to Regina's municipal heritage committee, the grave site — west of the city — has not been used in over 100 years.
Committee member Don Black said Monday that research has revealed attempts, in the past, to protect the site.
"They wanted the federal government to take some responsibility for cleaning up the site, maintaining it, honouring the lives of the kids that were in there," Black said. "That was from 1922. We have no record of the response, but looking out at it there wasn't much of a response."
It is believed the cemetery has well over 22 graves, including three graves for children of the first principal of the school, a Rev. J. A. McLeod.
City officials have promised to consult with other levels of government and First Nations on how to proceed.
A report is expected on the possible options by the end of 2013.
The cemetery is located just southeast of the intersection of Dewdney Avenue and Pinkie Road, on Regina's western edge.
The Regina Indian Industrial School operated between 1891 and 1910. It was then converted to a municipal jail and, later, it was used as a home for delinquent youths. It burned down in 1948.
The school, which had a residential component, was first operated by the Foreign Missionary Committee of the Presbyterian Church of Canada, under a contract with the federal Department of Indian Affairs.
According to historians, the school was one of many efforts by officials of the day to encourage assimilation of First Nations people.
The current owner of the land has told officials that he is aware of the cemetery and "fully respects the heritage value and sacred nature" of the site, according to a report by the city.