A ranger shot the three-metre saltwater crocodile near a billabong at Gumarrirnbang outstation, about 110km south-west of Maningrida and 340km east of Darwin.
Police say the remains have not been identified and investigations into the girl's disappearance are continuing.
The girl was reported to have been taken by a crocodile while swimming with her family at Gumarrirnbang outstation yesterday afternoon.
Senior Sergeant Shaun Gill said the crocodile was shot just before noon.
When it was examined, police found what it thought to be human remains inside the crocodile's stomach.
"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.
Sgt Gill said officers had worked under difficult conditions.
"This is a heartbreaking outcome for the family and the community," he said.
Earlier Senior Sergeant Geoff Bahnert said extra police officers had joined the search, after efforts last night failed to find the little girl.
"A full search of the billabong and the area where she went missing will be conducted today," he said.
"We have members that have travelled overnight from Darwin, members of the Territory Response Group, members of the Marine and Fisheries unit, as well as Northern Territory Parks and Wildlife rangers who ... [will] join Maningrida members who remained on site overnight."