The fish kill happened on the Brownsmills stream and was spread over a five kilometre stretch.
The agency say they cannot confirm the cause of the fish kill at the moment and have launched an investigation.
Species of fish discovered dead include brown trout and eel.
Inland Fisheries Ireland first became aware of the issue yesterday when a member of the public informed staff of seeing dead fish in the stream.
IFI have taken fish and water samples for analysis; Cork County Council Environmental Department are assisting with the investigation.
