The body of Sean Cole was recovered from crocodile-infested waters of the Mary River Wilderness Retreat, despite warnings against swimming there.
The 26-year-old was part of a group on a 30th birthday camping trip when he and a friend decided to swim across a river with one of the highest numbers of saltwater crocodiles in the world.
Onlookers reported seeing the animal, believed to be nearly five metres long, moving in the river with Cole's body in its jaws.
Northern Territory Police senior constable Wade Rodgers said his body was found early on Monday in the area where he had been last seen.
"Our thoughts are with the family during this very difficult time," he said.
Mr Cole's friend survived the attack.
The Northern Territory News said a survey three weeks ago counted four crocodiles over four metres in the area and 10 to 12 of the reptiles measuring more than three metres.
Parks and Wildlife Ranger Tom Nichols said four crocodiles had been shot, including the one believed to have been responsible for the attack.
"Any animals that were in that range which we believed to be a possible target in the area where the accident took place, we usually take them out for simple reasons," he said.
"We do autopsies on those and it's also closure for the families if there's anything there."
Glen Spearing, Cole's friend from the University Rats Football Club, told the Australian Broadcasting Corporation it was very strange for Cole to go swimming in a river known to have crocodiles.
"I think myself along with everyone else, when we found out we honestly didn't believe that it would have been Sean, we would have expected it to be almost anyone else in the club but Sean," he said.
"[It] just seemed extremely out of character for him."