The unidentified boy was swimming near Port Bradshaw when the crocodile suddenly grabbed the boy Saturday afternoon, the Australian Broadcasting Corp. reported.
Children at the scene began screaming and the boy's family and others rushed to the water and tried spearing the crocodile, described by police as "large," but it vanished with the boy.
Police and wildlife rangers fanned out and searched the creek until midnight, the report said. Several shots were fired at one crocodile, but it submerged and disappeared, the officers said.
Officials said residents of the town had been feeding the crocodile, which would reduce its fear of humans.
Three weeks ago, another child in the Northern Territory was taken and eaten by a crocodile, the broadcaster said.