Fears have been expressed that the native oyster could be wiped out on both Lough Foyle, between Co Donegal and Co Derry, and Lough Swilly in Co Donegal, threatening the livelihoods of more than 200 people.
The appearance of the disease bonamia ostreae in Lough Foyle is equivalent to an outbreak of foot-and-mouth disease on land, the Lough Swilly Wild Oyster Development Association said in a statement.
Chairman Alex Carlin said the discovery of bonamia, which has devastated wild oyster fisheries throughout Europe, must be treated as a crisis by the Minister for the Marine, Pat the Cope Gallagher.
Putting the impact of the disease in perspective, he said that bonamia had reduced French wild oyster output by more than 80 per cent over the last 25 years.
Mr Carlin said his association had been warning for some years that Lough Foyle was at risk of cross-contamination.
"There has been very active movement of trawlers and other vessels, such as mussel-seed carriers, from various bays in Ireland and elsewhere to and from Lough Foyle. Such movement would not be allowed on land if there was a risk of cross-contamination such as foot-and-mouth or BSE.
"We have had to fight every inch of the way to protect the Lough Swilly wild oyster fishery," Mr Carlin added. "We cannot stand back now and let the Swilly be destroyed by cross-contamination from the Foyle or elsewhere. "
The native oyster industry is worth an estimated €3 million annually to the Donegal economy. Most of the production goes to France.
Mr Carlin said local fishermen had invested heavily in developing the native oysters. "These people have money tied up in boats and now fear that their livelihoods could be wiped out."
The association is calling for an embargo on all vessels entering Lough Swilly from Lough Foyle, so that the outbreak of bonamia in the Foyle does not spread. "Allowing vessels of any description to move between a diseased bay and one that remains disease-free would be negligent," he claimed.
He urged the Minister for the Marine to declare Lough Foyle a shellfish "disaster zone", saying, "Lough Swilly is the next disaster waiting to happen."
In recent years, there has been a big increase in the cultivation of farmed oysters, known as gigas or Pacific oysters, which are not affected by the disease. However, the number of self-seeding native oyster beds has declined significantly, prompting fears about the survival of the native species.
The bonamia parasite was first observed in Normandy, France, in 1979 and has since spread to other European countries associated with transfers of oysters.
The Department of Communications, Marine and Natural Resources confirmed yesterday that "pending the confirmation of the test for bonamia, no approvals will be given in Ireland for movements of shellfish in to or out of Lough Foyle".
The Marine Institute has acknowledged the presence of a suspect organism in Lough Foyle and says it is investigating a potential case of bonamia ostreae. It stresses that the disease has no impact either on other shellfish or on human health. However, it affects the taste or edibility of the oyster and can result in heavy mortalities in the affected stocks.