English Nature is concerned that fishing boats could be damaging what has been described as the South West's equivalent of the coral reefs.
Divers say the scallopers plough the seabed up
It is holding talks with the owners of scallop fishing boats which have been dredging in the Fal Estuary, home to the UK's biggest expanse of the rare coral-like seaweed, maerl.
The area has been declared a special conservation area because it provides a breeding and feeding ground for other species.
Scallopers from Falmouth and St Mawes deny they are damaging the area.
Over the past few days, people in Falmouth say that a small fleet of scallopers have been dredging the seabed.
We have got nothing against scalloping, but this area is protected
They are furious and say the dredging nets, which are scraped along the seabed, are destructive.
Diver Steve McEwen said: "As divers, we have seen what a scallop dredger does. It ploughs the bottom up.
"We have got nothing against scalloping, but this area is protected."
But one group of scallopers who are based in Falmouth and St Mawes deny they are damaging the area.
They say they are using a deep channel which keeps them off the maerl bed.
Spokesman Clinton Powell said: "This has been blown out of all proportion.
"English Nature are concerned that we are going to kill the banks, which we are not."
The two sides now say they are working on ways to protect to maerl beds and there will be further meetings.