Sewage bacteria, thought to be E. coli, was found in the Camel Estuary, St Austell and Falmouth Bays, said the Food Standards Agency (FSA).
The FSA said it was “monitoring the situation” but the shellfish beds would remain closed.
David Jarrard, of the Shellfish Association, said: “The industry treats food safety as paramount.
“But I was astonished with these results, we have never seen any of this magnitude before and I just don’t believe them.
“The results we have had are akin to raw sewage and for that to happen in one river might be possible but to find it in all these areas is inconceivable.”
It has asked the FSA to disregard the results while an investigation takes place.
An FSA spokesperson said: “The results are unusually high which is why they require further investigation.
“We are monitoring the situation by taking further samples but until we have evidence to the contrary the beds must remain closed to protect public health.”