An unknown flesh-eating disease has killed millions of dollars worth of Pacific oysters in Port Stephens, and has caused financial devastation for many growers.

The Department of Primary Industries said yesterday it was also investigating mysterious deaths of previously unaffected Sydney rock oysters.

The department's scientists are trying to identify the disease to curtail any further damage to the industry.
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There is concern the incident at Port Stephens, along with the recent Hawkesbury River oyster deaths, may result in an oyster shortage in NSW.

Many growers told the Newcastle Herald the disease, which first emerged in January, had ruined their 2013 winter crop as well as next year's crop.

"It's pretty much wiped me out - it's had a massive impact on the industry," Lemon Tree Passage grower Paul Merrick said.

He has lost 80 per cent of this year's crop, worth $200,000.

The disease, which was first noticed in January, is not related to Pacific Oysters Mortality Syndrome.

This destroyed Pacific oyster supply around the Hawkesbury River.

Algal sampling by the Department of Primary Industries showed levels of algae Pseudonitschia is three to five times higher than in previous years.

"Pseudonitschia is not noted as a risk to shellfish but sometimes these blooms can irritate the oyster's gut lining, which could exacerbate any pre-existing conditions," a spokeswoman said.

"The Department of Primary Industries is also assessing water-quality data to try to identify factors which may be affecting oyster health."

She added growers affected by natural disasters or disease events could lodge an application for a fee waiver for financial hardship.

Port Stephens oyster growers' industry representative Richard Hamlyn Harris said growers want to know the cause of the disease.

"It's certainly very strange - I haven't come across a set of circumstances like this," he said.