It has been ordered not to accept any more remains.
The development comes after a separate investigation at a funeral home on Chicago Southeast Side found 56 decomposing bodies and more than 50 cremated remains.
Comptroller Susana Mendoza's office said late Saturday it was alerted about possible violations at the crematory located on Bohemian Cemetery grounds late afternoon on July 22.
Their office staff visited the site first thing in the morning on July 23, and found multiple equipment failures and some human remains waiting to be cremated that were not maintained at the proper temperature.
Mendoza shared statement on the investigation, saying in part, "At the time of our visit, 35 individuals at the facility were waiting to be cremated. This has been completed and nearly all the cremated remains have been returned to their respective families. The investigation is ongoing and potential disciplinary action is being discussed."
Meanwhile, investigators are still working to piece together the situation at South Chicago Chapel.
Saturday night, ABC7 learned Chicago police found more than 50 containers with cremated remains inside.
The Cook County Medical Examiner's now has those remains as police work to contact next of kin.
Close to 60 decomposing bodies were found at South Chicago Chapel on Thursday.
As the other investigation at Bohemian continues, the IOC says cemetery burials and cemetery visiting hours have not been affected and remain unchanged.
ABC7 is working to determine if the Bohemian facility is linked to the investigation at South Chicago Chapel.