The seven-year-old girl was swimming with other children and an adult at a local waterhole at the Gumarrirnbang outstation, 100 kilometres west of the remote community of Maningrida, when a crocodile attacked on Friday afternoon.
She was last seen being dragged under the water by the animal, which had also attacked the man who had been with her in the billabong.
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A three-metre crocodile was shot dead in the billabong just before noon on Saturday, Senior Sergeant Shaun Gill of NT Police said.
When it was examined, they found what is thought to be human remains in its stomach contents.
"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.
