The creator of a fish-based fertiliser has warned carp numbers in the River Murray have been vastly underestimated and that culling them could leave a stinking problem.

Harold Clapham created Charlie Carp 15 years ago as a way to harvest the pest to produce a beneficial by-product.

"We do between 350 and 400 tonnes of carp per year," Mr Clapham told 891 ABC Adelaide's Ian Henschke.

"We have the capacity to handle significantly more, but we are a demand-driven business."

In previous carp kills he has been involved in, Mr Clapham said the numbers of fish expected was always underestimated.

"Every time that we get told to expect 50 tonnes of carp, we get 100," he said.

"Not on one occasion have they ever fully estimated the full extent of the kill, the damage, and the number of carp involved."

Mr Clapham said he fully supported plans to rid the River Murray system of carp through the proposed introduction of a targeted herpes virus dubbed "carp-aggedon".

Carp is to be targeted in mass culls but concerns are held for the amounts of dead fish that will be produced. ( Cameron Atkins: ABC News )

"It's an issue that we have been harping on for a lot longer than a lot of other people," he said.

"We are supportive of anything to reduce or potentially eradicate the carp."

But Mr Clapham feared a mass cull would produce huge amounts of rotting fish.

He said researchers needed to concentrate on areas of highest populations first and ensure the biomass was contained and processed quickly.

Management contributing to carp population

Mr Clapham said he believed the environmental water flow and licensing management of the Murray-Darling Basin was contributing to the unmanageable carp population.

"There is no doubt that environmental watering and flows are affecting and proliferating carp numbers," he said.

European carp was introduced into Australian waters more than a century ago and was discovered in the Murray-Darling Basin in the 1980s.

Prolific reproducers, a mature female carp can produce up to 1.5 million sticky eggs which can float along watercourses and spread the population to new areas easily.

Female carp can produce up to 1.5 million sticky eggs. ( Supplied: Danswell Starrs )

Mr Clapham said during the millennium drought, numbers of carp fell significantly in the system.

His company sourced carp stocks only in the South Australian leg of the Murray during that time.

"When the drought broke [we saw] the greatest increase in numbers and the proliferation of fish all the way back up the system to our backdoor in Deniliquin," he said.

Mr Clapham said in the past six months the general size of fish he received per tonne had reduced, with large numbers of younger fish being caught.

A pile of carp from a cage trap in the Murray-Darling Basin ( Supplied: Invasive Animals Cooperative Research Centre )

"One of our biggest suppliers of carp is Lock 1 in South Australia (at Blanchetown)," he said.

"They get up to two-and-a-half to three tonne of carp per day out of their carp cage."

Cleanse the river from the mouth to the source

Mr Clapham suggested it would be best to eradicate carp from the Lower Lakes and Goolwa area before moving up the river.

"If something were to go wrong, it's easier to control it from the base upwards," he said.

The by-product from 2.5 tonnes of carp is 4,000 litres of fertiliser.

Mr Clapham said although his company would be able to quickly process fish as a result of a cull, he did not want the answer to one problem to create another.

"We could process thousands of tonnes of carp quite comfortably, but we don't want to produce a whole heap of government-subsidised fertiliser," he said.

"That ends up having a negative impact on commercial fertiliser businesses out there."