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Otago Regional Council director of resource management Selva Selvarajah said the problem was "really bad" in Otago.
"It's a widespread regional problem. We have six sites on State Highway 1 that some trucks aren't using. Central Otago is one of the worst affected areas."
Dr Selvarajah said the transportation of large numbers of dairy cows from Southland to areas such as Upper Clutha and Hawea for wintering was also affecting roads, as there were no effluent collection points after Raes Junction.
Stock effluent spillages on to Otago roads had increased during the winter feeding and grazing period, leading to increased concerns about the health and safety hazard for pedestrians, cyclists, motorcyclists and road workers as well as risks to drivers from obscured vision and slippery road surfaces.
Last year, in a joint operation with Environment Southland, police stopped stock trucks and checked for effluent discharge before and on Gypsy Day, when thousands of cows were being transported for wintering.
In a statement released last week, Environment Southland chief executive Rob Phillips said the council would reconsider its use of the Resource Management Act in its approach to stock trucks discharging effluent on to roads. The move follows a judge's decision to award costs against the council on a case heard last month.
Judge Jeff Smith ruled that the council must pay $5000 towards the legal costs incurred by Euan Shearing Contracting Ltd in preparing its defence relating to an alleged discharge of effluent from a stock truck on May 31 last year. The council had issued a $750 infringement notice against the shearing company, which took the matter to court.
Environment Southland withdrew the prosecution and the company sought costs.
In his ruling, Judge Smith noted that the case was "novel" in that it sought to prove the principle that a discharge of effluent from a vehicle could constitute an offence under the Resource Management Act.
Asked if the decision against Environment Southland affected the Otago Regional Council, Dr Selvarajah said the council had considered a similar approach.
"We did consider that approach for the oncoming season ... we have our multiparty strategy and will consider whether enforcement action will have to be taken during the oncoming season."
Early last month, the regional council convened a meeting of those involved in the movement of stock, including police, the New Zealand Transport Agency and Federated Farmers, to discuss how to reduce the hazard caused on roads by stock truck effluent spills.
Dr Selvarajah said the council would encourage farmers to manage stock in a way that reduced effluent on trucks, working with transport groups to ensure sufficient collection on trucks.
He said the "multiparty" would consider what actions to take in order to combat the problem, and planned to meet sometime in the next six weeks.