The Federal Government has been accused of deception after the Department of Agriculture revealed it had detected the highly destructive white spot virus in imported supermarket prawns this year.

After a Four Corners investigation questioned the effectiveness of border security last month, the Government announced that imported raw prawns tested in shops from the Logan River and Brisbane region were virus free.

"So far, touch wood, there has been no evidence that the new import protocols have failed us, that any of the virus or any of the affected prawns have brought the virus into Australia," Senator Barry O'Sullivan told ABC Radio last month.

But what the department did not tell the media was that tests of prawns being sold at retail outlets in Sydney and Melbourne this year did find white spot infected prawns.

The Government has now confirmed that two of 101 retail samples returned strong positives for white spot disease, while another four returned weak positives.

A spokesperson said the tests were conducted between May and June and the report was finalised on July 10.

This is the first time since the Federal Government beefed up biosecurity that it has admitted to the media that imported prawns infected with white spot disease were found in Australian retail outlets this year.

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Scientist claims government was deceptive

A University of the Sunshine Coast expert in marine animal genetics Wayne Knibb said the response to his findings was "deeply, deeply worrying".

Professor Wayne Knibb has tested supermarket prawns for white spot. ( ABC News: Megan Kinninment )

He said that when independent groups such as himself showed the presence of the virus DNA in the supermarkets, the department's reaction was to "try to rebut that critical information, to denigrate our methods, all the while sitting on their own information that suggests that our results were perfectly valid".

"They knew at the time of criticising our results, from their own work, that the virus DNA and likely living virus was in the supermarkets," he said.

Professor Knibb, a former principal scientist with the Queensland Government, had his methods questioned by the Federal Government when he found traces of the exotic virus in 30 per cent of prawn samples purchased from 10 major retail outlets in South East Queensland this year, after import conditions were tightened.

It described his tests for the Four Corners report as "flawed" because "cooked, breaded, battered and crumbed prawns were not required to be virus-free".

But from September, under new import conditions they will need to be partially cooked.

"We're actually playing Russian roulette and from time to time we pay the penalty of playing this dangerous game [in that] we get an outbreak or we have a likelihood of another outbreak," Professor Knibb said.

White spot disease in giant black tiger prawn, showing classic white spots on the carapace. ( Supplied: DV Lightner, Australian Government )

"We're trying to import 50,000 tonnes of green prawns into Australia, there is no method we know in science that you can test every little thing.

"Couple that with the entrepreneurialism of importers [and] you've got a real trouble of providing into Australia clean prawns.

"We don't have the same approaches to beef or chicken, because we're worried about foot and mouth."

Disease no threat to people

The white spot virus is not harmful to humans.

But it is lethal to prawns in ponds.

Seven prawn farms at Logan, near the Gold Coast, had to destroy all of their stock when the disease struck in 2016.

The source of Australia's outbreak has never been confirmed.

But in December last year a report by Australia's inspector-general of biosecurity, Dr Helen Scott-Orr, found a major biosecurity failure likely led to an outbreak.

She said a litany of failings allowed huge amounts of white spot-infected prawns to be sold in supermarkets.

Some infected prawns had been used as bait in the Logan river, upstream of the water intakes to the prawn farms.

Dead prawns on a Logan River farm in the aftermath of the 2016 white spot outbreak. ( Supplied: DIGFISH )

Biosecurity increased at borders

More than a $100 million of taxpayer money has since been spent on compensation, clean-up, monitoring and increased border security.

Containers of imported prawns are now required to be tested for the virus at the country of origin and again when they reach Australia.

"They did let us know on July 10 that there had been two positives out of Melbourne (retail outlets) and that they were following that up.

"So they've let us know but we don't know who the importers or exporters are or the type of prawns," Kim Hooper, the executive director of the Australian Prawn Farmers Association said.

"There's only a limited amount of information that we're getting and for us even one positive is not good enough.

"We don't want to stop importation of prawns, I'll be very clear about that.

"What we're asking for though is that those raw prawns be cooked so that we get the same accessible level of protection that is afforded to other industries such as chicken and pork."

Australian Prawn Farmers Association executive officer Kim Hooper believes prawns should be cooked before being allowed into Australia. ( ABC News: Tom Forbes )

The Federal Government commenced action against nine importers that brought in around 70 per cent of Australia's raw prawn imports in 2016.

Ten have had their Approved Arrangements revoked or suspended.

Seven entities have had a total 23 permits revoked.

The Department told the ABC it had consistently explained that it 'cannot guarantee that no prawns with white spot syndrome virus will ever arrive in Australia.'

"Enhanced import conditions for imported prawns and prawn products aim to reduce any biosecurity risk to an acceptable level which is very low but not zero," the department said in a statement.

In contrast the Queensland Government has taken a different approach.

A Movement Control Order remains in place to try and contain the white spot virus in south-east Queensland. ( Supplied: Queensland Department of Agriculture and Fisheries )

When white spot was confirmed in the wild in Moreton Bay it imposed a movement restriction order for raw wild caught prawns, crustaceans and marine worms between Caloundra and the New South Wales border.

Last month a Gold Coast bait supplier was fined $10,000 for transporting wild caught raw prawns carrying the white spot syndrome virus outside that zone.

Eric Perez from the Queensland Seafood Industry Association believes the differences between the response from the state and federal governments boiled down to international trade.

"If we put restrictions on then suddenly, 'Oh well you export to our countries, what if we put restrictions on what you export out' so it is a trade issue," Mr Perez said.

"The Government will never admit to that but that's the reality that we face.

"Unfortunately our industry has been sacrificed on that altar of trade and it's never been good enough.

"Now we've got this exotic disease in the country and hopefully in the next two years we'll see it eradicated from our waters, that's our hope."

Despite the heavy financial toll on their businesses, there has been no compensation for commercial wild caught fishers.