Police say the girl was fishing with her family in the Blythe River in Arnhem Land when the attack happened on Saturday night.
Police officers believe they will be able to find the girl's body, and the crocodile that was responsible for the attack which will be killed.
Senior Constable Tony Martin has told the ABC, the attack has devastated the little girl’s family.
“They had gone to the water's edge to collect water. The girl apparently had gone ahead of the parents. And in the darkness they heard a big splash and the child was gone.”