Oysters are dying in Carlingford Lough because of a virus linked to the hot weather.
The Department of Agriculture and Rural Development (Dard) said ostreid herpes was detected yesterday following a sample of dead pacific oysters.
Dard said there were no other oyster mortalities reported.
The Food Standards Agency also said it is not aware of any reports of human illness associated with the virus.
"The deaths appear to be linked to the hot weather," said a Dard spokesman. "The virus appears to lie latent until water temperatures reach 16C, at which stage the oysters begin to die very quickly.
"Temperatures have risen to 20C in recent days which has significantly reduced dissolved oxygen levels in shallow areas where oysters are grown.
"Such temperatures are not unusually warm, but combined with the virus, conditions have resulted in oyster mortalities."
South Down SDLP MLA Sean Rogers said some oyster farmers had been very badly affected. "One farmer has lost 80% of his stock in just two days, which is essentially three years of hard work in often very difficult conditions," he said. "It's assumed that these losses are linked to the unusually high water temperatures.
"We could potentially be looking at the total decimation of oyster farming as we know it locally."