Plans for an extension to the Silver Hill Foods facility in north Monaghan have been appealed to An Bord Pleanála.
Inland Fisheries Ireland has raised concerns over the treatment of waste and waste water at the planned facility.
The Emyvale duck company was granted approval for this extension by Monaghan County Council in July.
It consists of a new facility for chilling, plucking and processing, offices, canteen and hygiene facilities.
Also included is a single storey conveyor belt connecting to the existing factory, an offal processing facility, underground water storage tanks and car parking.
Inland Fisheries Ireland says it has concerns about the treatment of waste water and duck waste from the site.
Silver Hill has included a 15 hectare wastewater drip irrigation system in the plans, however in its submission to the County Council IFI said this type of system can be 'problematic' as factors like ground conditions and weather can impact on its effectiveness.
It has appealed the project to the planning board, which is to make its decision by mid-December.