"Further forensic testing will be conducted in Darwin to determine if the remains are human and, if found human, the identity of the person," Sgt Gill said.
Police will prepare a report for the coroner and an investigation will be launched.
Members of the community had been searching for the girl from first light on Saturday, joined by the Territory Response Group, the Water Police Section and a ranger from the Crocodile Management Unit.
Sgt Gill said officers had worked under difficult conditions.
"This is a heartbreaking outcome for the family and the community," he said.
Crocodiles are not thought to have been seen in the area previously and the community believed the billabong to be safe.
-AAP