Recreational fishers are being advised not to eat shellfish caught in the Gippsland Lakes with fears they may be affected by a natural toxin.

Just days after dozens of people fell ill from salmonella in packaged salad, Victorian health authorities are dealing with a new toxic food threat - from shellfish caught in the Gippsland Lakes.

Recreational fishers are advised not to eat shellfish and mussels from the lakes until further notice because of the possibility a toxin produced by a type of algae has affected them.

The Department of Health and Human Services says the likelihood of a serious risk to human health is low but the advice is a precaution until further testing confirms if the shellfish are safe to eat.

"Further advice will be provided to the community as soon as these results are available, probably by the end of the week," a department spokesman said.

Swimming, fishing, boating and other water activities are not affected.

The Department of Environment, Land, Water and Planning testing identified the presence of the algae, Pseudonitzschia delicatissima, in sites at Metung and Paynesville's Eagle Point.

The algae is normally found in low levels in coastal waters and some produce a toxin, domoic acid.

The Department of Health advises that strains of the algae that produce the toxin are not common in Australia and have only produced toxins at low levels.

But if seafood eats this algae, the toxin can accumulate and cause illness in consumers.

Mussels and other shellfish are more likely to accumulate this toxin as they are filter feeders.

Other fish are unlikely to accumulate the toxin at significant levels.

Anyone that has consumed mussels or other shellfish from the Gippsland Lakes and has gastroenteritis (usually within 24 hours of consumption), nausea, vomiting, diarrhoea, or abdominal cramps, should see their doctor, the health department spokesman said.

Those who experience neurological symptoms (usually within 48 hours of consumption) such as headaches, confusion, short term memory loss, or breathing difficulties and seizures should seek immediate medical attention, he said.