The Otago Regional Council's proposed water quality plan aims to stop animal waste from being pumped into rivers.
The company's Finegand plant, near Balclutha, discharges treated effluent into the Clutha River.
Silver Ferns chief executive Keith Cooper says it has resource consent to discharge the treated effluent, which includes animal effluent, and is seeking to clarify that it is not caught by the proposals.
He says the future of the meat processing plant, one of the country's biggest, is not in doubt.