"We regard it as serious and we're taking our time to get the decisions correct," Rangitikei Mayor Andy Watson said.
Rangitikei's infrastructure manager Hamish Waugh said council had improved its data reporting in the past 12 months.
"I acknowledge that it wasn't up to scratch in the past."
The council was compliant in 14 of the 16 conditions related to the MWTP. "The plant does actually work. It's not a dog."
The two conditions which consistently fail compliance are ammonia levels and discolouration caused by the leachate.
The issues have been known for several years. A 2007 report noted the Bonny Glen leachate was having an effect on the plant and measures to reduce the impact include changing the point at which the leachate was dumped into the system and installing floating wetlands. None have been effective.
"It's not going to be cheap. It will be a seven-figure cost for someone to bear," Mr Waugh said.
Horizons chairman Bruce Gordon questioned why the council ever accepted leachate from Bonny Glen.
When RDC applied for consent to discharge into the Tutaenui Stream it was required to list all sources of waste, and leachate was not one of them. "Had it been, you probably wouldn't have got the consent," Mr Gordon said.
Environment committee chair Colleen Sheldon asked if the MWTP would need upgrading - an option RDC is considering - if it stopped taking leachate from Bonny Glen.
"Probably not," was Mr Waugh's response.
Horizons Councillor Murray Guy questioned whether councils were best placed to make those decisions on accepting industrial waste.
"[We have] councils trying to make decisions that benefit industry and commerce, but have consequences for ratepayers."
Earlier in public forum, Marton man Geoff Mills said institutional problems within RDC needed to be addressed.
Mr Mills has worked in the water and wastewater field throughout his career and said RDC had not followed due diligence in terms of analysis before accepting the Bonny Glen leachate, and failed to ascertain its environmental impact since. He said regardless of whether the leachate continued to be put into the MWTP, there had been significant costs on ratepayers and "potential risk of the ratepayer having to bear long-term costs. A technical fix is only part of the answer."