Investigators said they found the remains Thursday inside a box that was behind other containers and piles of trash in the detached garage.
An autopsy conducted Friday was inconclusive, and DNA tests will be needed to determine if the remains are of 19-month-old Elaina Steinfurth, a county coroner said. Investigators, though, were confident that what they feared was true.
"We found what we believe may be baby Elaina," said Toledo Police Chief Derrick Diggs.
The home and the garage where the box was located belong to the family of a man who had been dating the girl's mother.
Both the mother, Angela Steinfurth, and her now-estranged boyfriend, Steven King II, are in jail and accused of obstructing justice. No charges have been filed since the remains were discovered.
Steinfurth and her two daughters stayed with King at his family's home on June 1, investigators said. The girl's father went to the residence to pick up his two daughters the next day, but only Elaina's 4-year-old sister could be found.
Investigators have said Steinfurth knew Elaina had been seriously injured and didn't seek medical help. They would not say what type of injuries the toddler had or who caused them.
Steinfurth has been in jail since mid-June.
King was charged in July with lying to investigators about the child's disappearance. He told reporters after his arrest that he is innocent. A message was left with his lawyer.
Authorities, including the FBI, have searched homes, vacant buildings and the Maumee River near downtown Toledo for any sign of Elaina over the past three months. Volunteers also have looked through neighborhoods and parks.
Officers searched both the home and the garage in the days after Elaina disappeared.
They went to back to the home Thursday and removed the box with the remains, just hours after King appeared in court at a hearing where his trial date was scheduled.
Angela Steinfurth's stepfather, Richard Schiewe, said the box was not in the garage the day after the little girl was reported missing. He said he went into the garage with police when they searched the building.
"That body was not in the rafters," he said Friday. "Somebody went and got that body and put it in there."