Cpl. Jeremy Tinkel said the boy's family reported to police that he was missing on Friday.
How he died is not clear, and investigators are not sure whether foul play is involved, Tinkel said.
Tinkel said a civilian by the pond Sunday afternoon spotted the body floating out from shore, but the corporal would not elaborate on the circumstances of the discovery.
Sheriff's deputies were sent to the pond in the Hamilton Meadows addition near Illinois and Noyer roads about 2 p.m., and the body was removed from the water. Tinkel described the pond as a retention pond or something similar, rather than a pond for swimming.
The sheriff's department and the Indiana Department of Natural Resources are investigating the case. The county coroner's office will try to determine the boy's cause of death.
Hamilton Meadows is west of Fort Wayne, just east of the Allen-Whitley county line.