Two earlier attacks claimed the lives of an 11-year-old girl and a 20-year-old man.
The boy, who was fishing at Adelaide River on Easter Sunday when the crocodile lunged at him about 10.30am (CST), managed to escape with only minor injuries.
He received stitches for a puncture wound to his hand at a local medical clinic.
"I believe that the boy was the only one who saw it so no-one knows whether it was a saltie or a freshie, or what size it was," said a police spokeswoman.
"It sounds like a croc just came out of the water and went chomp."
A trap was set in the area almost a month ago after a large saltie, believed to be about five metres, was spotted in the river.
The river is known for it's large population of saltwater crocodiles and is about 114km south of Darwin.
News of the attack comes a day before the NT government is due to release its revised crocodile management plan.
Safari hunting and widespread culling is under consideration, along with the removal of crocodiles from a 50-kilometre zone around Darwin.
Independent Member for Nelson Gerry Wood on Tuesday described the plan as "science fiction, not science".
"You will be doing it for ever and a day," he said.
"I am not against some culling but to have a 50km croc free zone doesn't make any sense, it's not practical and the amount of resources and finances that it would cost would be enormous...
"There has to be an element of common sense as well ... we have to learn to live with them."
Two fatal attacks have sparked debate about the methods to control the NT's crocodile population, recently estimated to be the highest in Australia at more than 80,000.
Last Friday, a man was fatally attacked a day before his 21st birthday while swimming across the Daly River, 150km south of Darwin.
The father of two, who cannot be named for cultural reasons, was swimming across the croc-infested river with his cousin.
A 4.3-metre crocodile believed to be responsible for the attack was destroyed the following day.
The reptile that killed 11-year-old Briony Goodsell last month is still at large.
The little girl was swimming with her sister and two friends when she was dragged under the water by a crocodile at Black Jungle Swamp, in rural Darwin.
ninemsn 14 Apr 2009
Again it is because of human stupidity that the animal kingdom MUST suffer.
The signs are CLEARLY visible and are there for a reason.
Animal Instincts 101 : Crocodile, primitive. Body in water = FOOD !!
As much as this is a 'tragedy / 'accident' the fundamental laws of nature are ignore by the so called 'intelligent' species.