The remains were found during a search of the home of Steven King, the ex-boyfriend of the child's mother, Angela Steinfurth, northwestohio.com reported.
Police said a box containing "immature human skeletal remains" was found in the garage, which police had previously searched. Cadaver dogs had been used in previous searches of the property, but police said Friday they were not allowed to enter the garage because of its condition.
The remains have been turned over to the Lucas County Coroner's Office.
King and Steinfurth both faces charges of obstruction of justice in the child's disappearance. They were the last people seen with the child before she disappeared.
King is scheduled to go to trial Sept. 16. He has pleaded not guilty.
Steinfurth appeared in court for the fourth time Wednesday. She is scheduled for another pretrial hearing Sept. 25.