Northern Territory police said the man was with a group celebrating a birthday at the Mary River Wilderness Retreat, about 110 kilometres (70 miles) from Darwin, on Saturday when he decided to plunge into the water.
"They were watching him swim across," senior sergeant Geoff Bahnert told AFP of the group.
"And they just saw a crocodile with him in its jaws."
Police conducted a search for the man, but were unsuccessful. The search was continuing Sunday, Bahnert said, adding that the largest crocodile at the site had been shot and killed as a precaution.
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