There are concerns the shooting death of a 5.2-metre crocodile will create a power vacuum in the local population — with warnings younger crocs will become "increasingly aggressive" as they fight for the position left vacant.

The male crocodile was found yesterday in a creek along the Fitzroy River near Rockhampton with a single gunshot wound to the head.

As a result the Department of Environment and Heritage Protection has issued an urgent warning for members of the public to be vigilant.

Biodiversity operations director Michael Joyce said the dead crocodile helped keep the river "in check".

"People need to clearly understand the death of this animal has changed the balance of the crocodile population in the Fitzroy and we can expect increased aggressive activity by younger male crocodiles," Mr Joyce said.

"That's because they will be competing to take the dominant position which is now vacant. I cannot stress strongly enough the need for all river users to be aware of the risks."

Police intend to carry out examinations on the crocodile. ( Supplied: Queensland Police Service )

Mr Joyce said the department did not believe the crocodile had been a problem.

"The simple fact of the matter is that he is a crocodile that does spend a fair bit of time controlling the river and controlling the young animals that are in the river — an important part of our ecosystem and he was certainly well outside of the crocodile management zone," he said.

Mr Joyce said it was deeply concerning to the department that the crocodile had been illegally shot.

He said the dead crocodile was not believed to be the same animal which is currently targeted for removal, about 3 kilometres upstream of Pink Lily Sands.

"Wildlife officers are continuing their efforts to remove that crocodile and a floating trap remains in place," he said.

"The animal we are targeting for removal is a 2.5-metre animal — much lower in the system and within the crocodile management area Zone C," he said.

"If this iconic crocodile had been reported to us, officers would have immediately taken steps to remove it, in accordance with the Queensland Crocodile Management Plan."

Mr Joyce said officers had been monitoring the Alligator Creek area due to reports in the past of crocodile sightings.

"Being a 5.2-metre animal, he's actually learnt to be very shy of people so someone might see him and report that, but actually getting onto him and seeing him is quite challenging.

"He would be very cautious and certainly he didn't come up in our latest surveys of that river," he said.

Offender faces jail, fines of more than $28,000

It is an offence under the Nature Conservation Act 1992 to take an estuarine crocodile without authority.

There are greater penalties in place for the unlawful killing of an "iconic" crocodile, which is defined as being 5 metres or more in length.

The maximum penalty for the unlawful killing of an iconic crocodile is more than $28,000.

Police are investigating the shooting death of the crocodile. ( Supplied: Queensland Police Service )

Police are now also appealing for information on the matter.

Acting Detective Inspector in the Capricornia Police District Luke Peachey said an autopsy was being conducted on the crocodile to give authorities more details.

He said offenders faced up to three years' imprisonment if found guilty of an offence under the Animal Cruelty Act.

"What we are doing is asking anyone with any information or knowledge on the cause of death of this animal to contact Rockhampton CIB and Crime Stoppers," Acting Detective Inspector Peachey said.