AFFCO and Hawke's Bay Regional Council have reached an agreement over the discharge of waste from the company's sheep and beef plant in Wairoa, into the Wairoa river.
Nearly three years ago, the company objected to conditions of a new resource consent and indicated it would take the matter to the Environment Court.
However after discussions with the council, AFFCO agreed to a mediation process to resolve the issue.
Council resource management manager Ian Maxwell says it's been a long process, but finally both parties have agreed to a new set of conditions.
He says the council is comfortable its standards are being met, but also that AFFCO is able to meet those standards without being penalised continually.
Mr Maxwell says the discharge still remains but it is controlled in a much more rigourous way than it has been in the past and there have been upgrades in a number of places.
He says there are stringent monitoring conditions attached to the consent that AFFCO would have to fulfil themselves and council has a number of its own monitoring sites throughout the region.
Mr Maxwell says the primary one is that AFFCO prepare a compliance report and that the council reviews and looks for conformance with its standards on a regular basis.