This was not disputed during the case but Fonterra challenged its criminal liability for the discharges.
Judge Dwyer, however, rejected its defences and found Fonterra guilty of the charge, which was laid by the Taranaki Regional Council.
At a sentencing hearing yesterday in the New Plymouth District Court, Fonterra was fined $192,000 over the matter.
In an unrelated case last week Fonterra was fined $170,000 for discharging wastewater into the Rangitaiki River on six different occasions.
The company had pleaded guilty to four offences relating to their wastewater irrigation system and two for overflows at their Edgecumbe plant.
The Rangitaiki River was polluted by the failures between September 2014 and April this year.
Bay of Plenty Regional Council pollution prevention manager Nick Zaman last week said the discharge of dairy wastewater directly into the river was disappointing.
"The Rangitaiki River is important for migratory and indigenous fish, it has whitebait spawning sites, and is culturally very significant to a number of iwi including Ngati Awa, Ngati Tuwharetoa, Ngati Whare, Ngati Manawa and Ngai Tuhoe. It's the pataka kai -- food basket for iwi."
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While noting that the circumstances behind the two prosecutions were "entirely unrelated", Fonterra's managing director of global operations Robert Spurway yesterday said the co-operative would "like to reiterate our regret for the impact of these issues on the Eltham and Edgecumbe communities".
"We take our obligations under the Resource Management Act seriously. Sustainable dairying is one of the core tenets of our business and we set high environmental standards for ourselves," Spurway said.
"Since 2013, Fonterra has taken a number of steps to ensure the circumstances that brought about the need for disposal in Eltham are not repeated. This includes adding more processing capacity as well as more robust by-product disposal options where required," he said.
"In Edgecumbe, we have implemented a number of new tests and controls on our extensive network of pipework, irrigators, pumps and hydrants, and will continue to invest in these to ensure we meet environmental best practice."