The man charged with killing a huge crocodile in the Fitzroy River has faced court in Rockhamption charged with unlawfully taking a protected animal.

Luke Stephen Orchard, 31, was arrested after police executed two search warrants at his Etna Creek home and seized a number of firearms on December 21.

The male crocodile was found with multiple bullet wounds, including one fatal shot to the head, in late September 2017.

Luke Stephen Orchard, 31, fronted Rockhampton Magistrates Court early on Saturday morning

Luke Stephen Orchard, 31, has been charged over the fatal shooting of a 5.2 metre crocodile

According to 9NEWS, Mr Orchard is expected to enter a plea on February 16, when he will return to court.

If found guilty, he could face a hefty fine of $$28,383.75 - the maximum penalty for unlawfully killing a protected estuarine crocodile.

WA Today revealed in December that several bullets were pulled from the crocodile's body during a post-mortem examination, and given to the rural Major and Organised Crime Squad to assist their investigation.

Detectives will allege that a search of Mr Orchard's property turned up 'two Marlin 336 lever action 30-30 calibre rifles, a quantity of ammunition and a number of electronic devices'.

Queensland Department of Environment and Science operations director Michael said they take wildlife crime very seriously.

He also emphasised that estuarine crocodiles have been protected under the Nature Conservation Act since 1992, and that it is illegal in Queensland to kill them.

The 31-year-old suspect will front court in January and faces a maximum fine of over $28,000

The body of the huge reptile washed up in the Fitzroy River at Etna Creek on September 21st

While some residents believe that a crocodile cull is necessary, Koorana Saltwater Crocodile Farm owner John Lever said the killing of the crocodile created more problems than it solved.

'The crocodile was probably the alpha-male in the area and because it is now dead, there will be a scramble amongst the other males to take his place,' Mr Lever said.

'It will take two or three years to settle down and the crocs will be more dangerous during this time because they will be fighting for territory, females and food.'