Rangers had targeted a crocodile with a distinctive scar near its snout as an extensive search for the NSW man near Cooktown entered a third day.
It is believed the man had been fishing with his wife and children at Annan River Bridge on Saturday afternoon when he fell into the water, failing to resurface.
Wildlife officers began surveying crocodiles in the area after revealing on Monday the "target animal" had a distinctive marking.
The search for the missing fisherman at Annan River has entered its third day. (HANDOUT/QUEENSLAND POLICE)
"There have been some suggestions that the crocodile may have a white scar on its snout," Department of Environment, Science and Innovation's Daniel Guymer told reporters.
Hours later, rangers confirmed a helicopter search had located the reptile in a creek 4km upstream from the suspected attack.
"Wildlife officers have humanely euthanised a large crocodile that is believed to be responsible for the fatal attack on the Annan River," the department said in a statement.
"The animal had markings on its snout that were consistent with it being the target animal.Â
"Wildlife officers are removing the animal from the creek and will hand it over to the Queensland Police Service."
Authorities on Monday expressed their sympathy to the missing man's family and friends during a "very traumatic time".
Police are rallying around the family, offering them "all available support for their wellbeing".
Rangers have been assisting police and SES volunteers with boats, drones and helicopters in the land, air and water search for the man.
Helicopters, drones and boats are being used in the search for the man. (HANDOUT/QUEENSLAND POLICE)
Wildlife officers on Monday revealed they were investigating social media videos that have emerged of people feeding a crocodile at a location that appeared to be the Annan River.
Mr Guymer said DESI was aware of the videos, describing it as "very, very concerning behaviour".
"It is very risky and it is very reckless. It is actually an offence," he said.
"If people are feeding this animal ...it will encourage that animal to stay in that area and that will present a safety risk."
Anyone with information can report to DESI anonymously, he said.
The penalty for deliberately feeding a crocodile is a $6452 fine.
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