He said solid waste was kept onsite, while the plant's wastewater was "Ph neutralised" and discharged into the wastewater treatment plant. Mr Houston said he had no idea who had dumped the material.
Affco's operations manager, Rowan Ogg, said his company was not responsible.
He said he was not sure if the council had been speaking to the company's Wanganui management, but he thought not.
Mr Ogg said the plant's solid waste was put through a sophisticated sieving process then put into onsite settling ponds.
He said it was not in Affco's interests to dump solid waste.
"For financial reasons, it's in our best interests to keep our wastewater as free of solid matter as possible. Our solid material does have some financial value," Mr Ogg said.
Councillor Ray Stevens said only a small handful of companies could potentially be responsible.
On Monday, Horizons Regional Council issued a formal warning to the Wanganui District Council for being in breach of region-wide rules, because of the plant's odour.
Meanwhile, Mark Hughes, council's infrastructure manager, said they would be giving public updates on the state of the ponds and progress with solving the problems every Monday, Wednesday and Friday.
"The odour levels have come down but they are still by no means acceptable," Mr Hughes said.
