Commercial shellfish harvesting has ceased in certain bays along the west and southwest coasts, after high levels of toxins were found during routine monitoring.
As a result, the public are being urged to only consume shellfish from reputable dealers.
The Marine Institute says the naturally occurring compounds can make people ill, even when fish is cooked, and it has advised against recreational gathering of shellfish.
The high toxin levels in question are common at this time of year, due to the presence of a microscopic plankton species in Irish waters.
These summer blooms occur naturally, due to longer day length and warmer temperatures.
But the toxins can accumulate in shellfish, causing a gastroenteritis-like illness when eaten by humans.
In some instances, consumption can lead to the less common, but more serious, paralytic shellfish poisoning.
In extreme cases, this can lead to muscle paralysis, respiratory failure and even death.
The Marine Institute said all commercial harvesting in affected areas is controlled since the problem was identified and alternative supplies of shellfish on the market are safe to eat.
In the meantime, people are being urged not to pick wild mussels, clams, cockles or oysters to minimise the risk.