Prawn farmers on Queensland's Gold Coast wiped out by an incursion of white spot disease are struggling to dispose of millions of dead prawns.

Since December, prawn ponds on four farms along the Logan River were pumped with chlorine to kill infected prawns and to stop the disease from spreading.

Paradise Prawn Farm director Ian Rossmann said he had up to eight million dead prawns on his farm that he didn't know what to do with.

"There are 350,000 prawns in each pond and the issue at hand now is to get the water drained out of those ponds and the clean up to start," he said.

"There are seven to eight million prawns on our farm but it also involves three other farms and one of them is a very big farm, it's quite a lot of issues we need to work through.

"We hope they will be disintegrating or rotting away."

Prawn farmers Elwyn Truloff, Simon Rossmann and Ian Rossmann have white spot disease on their farms ( ABC RURAL: Marty McCarthy )

Mr Rossmann said in addition to dealing with the dead prawns, farmers were unsure about the possible infection of other crustaceans in the area.

"One of the main issues is the little crabs that survived the chlorination, they are also a vector of the virus," he said.

"That is our major concern, to actually get rid of the little crabs first."

Mr Rossmann believes the clean-up should be the responsibility of Biosecurity Queensland, but acknowledged the need to follow strict quarantine rules.

"They [Biosecurity Queensland] came on to our farm and killed all of our product, and we always had concern about what would happen after with the clean-up," he said.

"The Biosecurity Act is a very powerful act, and it has to be, so we respect that."

Mr Rossmann said even if he was able to produce a crop this year, he does not know if he would be able to afford it.

"Compensation is not a word so far, so we are taking a total loss of $1 million dollars of destroyed crop and a loss of income for the year," he said.

"It looks like we will have to line our ponds with plastic and do lots of things that amounts to major dollars in new infrastructure."

Biosecurity begins clean-up of decontaminated ponds

Biosecurity Qld's Jim Thompson said there was a sense of urgency around the program due to the contagious nature of the white spot virus.

"It is new ground, and it's a massive operation, we realise that, but we are confident we can achieve success in terms of decontaminating these farms," Dr Thompson said.

"Phase one has been completed on five properties so all production ponds are treated and we're now moving into phase two, which is the disposal and decontamination, and that involves the removal of the water, and the removal of the decomposing prawn material that is at the bottom of those ponds".

Mr Thompson said it was hard to pinpoint exactly when the farms would be operational again, as the decontamination process would take several months to complete.

But the aim was to have the farms back in business by the spring season.

"This is the only chance that we've got, and we want to make sure that we take all opportunities to make this happen.

"The discussions about financial assistance are ongoing. We've been discussing with the prawn farmers themselves about the activities they've undertaken, and we've given an undertaking to assist them with that, and we're talking with the Commonwealth Government, and the industry, because this a shared responsibility about how we go forward here."