The fisheries board and Environmental Protection Agency (EPA) have launched investigations into the fish kill on the Kiltha River, near Castlemartyr.
Water and fish samples were taken from the river on Sunday after the dead fish were found 24 hours earlier.
A few months ago, anglers on the river expressed fears that salmon and trout stocks could be wiped out by discharges into the river which they say are emanating from a speciality cheese plant and a nearby waste treatment plant.
But, last night, management at the Dairygold grain storage facility came clean on their role in the incident.
In a statement, the co-op said: “Management of the grain storage facility acknowledge the possibility that some contaminant from the site may have entered the Kiltha River and may have caused the fish kill.
“Dairygold is carrying out its own internal investigation to determine all the facts and will co-operate fully with Inland Fisheries to ensure that any such regrettable incident can be prevented from reoccurring in the future,” the statement read.
Work was under way in recent days to clear out grain storage areas at the plant so the upcoming 2012 grain harvest could be accommodated.
The dead fish were first discovered by members of the public walking around Castlemartyr village on Saturday evening.
The Kiltha River runs between Mogeely and Castlemartyr.
The brown trout, juvenile salmon and lamprey eels were found over a four-mile stretch running from Mogeely Bridge, past Ightermurragh Castle, between Ladysbridge and Finisk.
The colour of the water had not changed in the hours or days leading up to Saturday evening.
It’s believed whatever entered the water was colourless and odourless.
“There were great salmon stocks this year, some of the best in 30 years,” the Womanagh Angling and Development Association’s environmental officer, David Burke, said. “We are devastated at what has happened.”
Locals have long claimed the Kiltha River is being harmed by emissions flowing from the co-op’s plant in Mogeely along with the county council’s waste water treatment plant at Castlemartyr.
Cork County Council admitted, earlier this year, there are “periodic operational issues with the waste treatment plant” but said that they had been remedied.
A council spokesman said that the current quality of final effluent was not at acceptable standard — although in compliance with the Urban Wastewater Directive.
Meanwhile, the EPA — which inspects the Dairygold-run cheese plant — has been made aware of excessive discharges from the Dairygold plant in the past.