Agriculture Minister Barnaby Joyce has accused seafood importers of “swapping prawns” to avoid disease detection.

An ongoing outbreak of the deadly white spot disease (WSD) threatens a large chunk of Australia's farmed prawn industry.

Mr Joyce recently suspended the importation of green prawns after infected product was found for sale in Australia.

But he now suspects suppliers of trying to thwart the ban.

“There's a strong case that people have been swapping prawns,” Mr Joyce told the ABC.

“It's just like doing urine swaps for rogue footy players.

“The [importers] were offering up a batch of prawns [for inspection] they knew full well didn't have white spot and taking the others in the back door.”

Criminal charges have been sought for Chinese importer Sino, and the Government says it is investigating at least four others.

“The prawn industry is about a $358 million a year industry between imports and domestic, and [Sino] were a major player and now they've got some major questions to answer,” Mr Joyce said.

“If they've done it, it's a criminal event and we'll nail them.”

Seafood importers say the holes in the quarantine system are well known, and that the import ban is doing serious damage to the industry.

Additionally, farmers whose stocks are infected with WSD are being forced to destroy tonnes of their prawns, worth millions of dollars.

Biosecurity Queensland has ordered some farmer to destroy prawns using chlorine, which causes them to leap out of their ponds gasping for air as the chlorine burns them and removes their oxygen.

The Prawn Farmers Association says it is highly dismayed that it takes a major outbreak of WSD for the industry's concerns about imported stock to be taken seriously.