The crocodile's body was found in the Fitzroy River in Queensland after suffering a gunshot to the head.
The government issued a warning that the killing could spark aggressive behaviour from younger crocodiles that would previously have been kept in check by the dominant male - but that would now be battling for dominance.
According to the Telegraph, Michael Joyce, southern wildlife operations director at Queensland's Department of Environment and Heritage Protection, said: "People need to clearly understand the death of this animal has changed the balance of the crocodile population in the Fitzroy.
"We can expect increased aggressive activity by younger male crocodiles. That's because they will be competing to take the dominant position which is now vacant."
The crocodile was taken to the nearby Koorana crocodile farm, where owner John Leaver said a five-metre crocodile had not been caught in Queensland for the last 30 years, according to the Guardian.
Mr Joyce said there were not a lot of crocodiles over five metres long, and that the crocodile that was killed is thought to have been between 80 and 100 years long.
Saltwater crocodiles have been a protected species since the 1970s. In Queensland, the maximum penalty for killing a crocodile is £16,600. However, the penalty for killing an 'iconic' crocodile, defined as being greater than 16.4ft (5m) in length is up to three in jail.
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