The 22-year-old was last seen by his family on Friday at Pirlangimpi, on Melville Island about 100 kilometres north of Darwin.
Police said local community leaders shot the crocodile dead yesterday in their hunt for the man, and biological material was found inside.
"At this stage it is unknown if the remains are human and testing will be undertaken," said Sergeant Antony Deutrom from the Northern Territory police.
"This is a very distressing time for the family and community."
In June, a man was snatched by a crocodile in front of terrified relatives while on a boat trip in the country's north.
It was the first fatality since January, when a 12-year-old boy was seized by a crocodile in the Kakadu national park.
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