An extensive search was launched after the girl went missing while swimming at Mango Creek near Palumpa, about 360km south west of Darwin, late on Tuesday.
Police said initial reports stated the girl had been attacked by a crocodile.
A shirt believed to be belonging to the young girl was found earlier on Thursday, 36 hours into the search, the ABC reported.
A few hours later police announced that human remains had been located.
"Northern Territory Police have located remains near Palumpa believed to be that of a missing 12-year-old child," police said in a statement on Thursday.
The girl's disappearance sparked a large scale land, water and air search with up to 40 locals at one stage assisting as they scoured the banks of the small creek.
Senior Sergeant Erica Gibson said the discovery of the human remains had hit the girl's family - and community - hard.
"This is devastating news for the family, the community and everyone involved in the search," she said in a statement.
"Police are providing support to the family and community, along with the first responders who attended the scene."
