Federated Farmers has accused Fish & Game of using leading questions in a survey on clean waterways.
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The agency commissioned a survey on public attitudes on protecting rivers and lakes from pollution.
The survey, by the research group Colmar Brunton, said 82 percent of respondents would support mandatory environmental standards for New Zealand's waterways, enforced by local councils.
But Federated Farmers water spokesperson Chris Allen said the group asked leading questions.
A more balanced approach, referring to urban as well as rural areas, would have produced a different result, he said.
The question from Fish and Game read: "Mandatory environmental standards would mean regulating intensive farming practices. As a result, there would be less contaminants in our waterways, but dairy farmers would likely have to change how they farm. Do you think that mandatory environmental standards should be introduced in NZ?"
Mr Allen said this was a biased form of questioning designed to elicit the answer Fish and Game wanted.
He also accused Fish and Game of frightening people about water quality that was better than had been claimed.
"All they are doing is scaremongering a huge amount of the population.
"We have got really good water levels and we have good quality water in many of our waterways," he said.
Mr Allen said Fish and Game might have needlessly scared off many people from swimming, by suggesting it was unsafe when that was untrue.
"We are working hard with the farming sector, we are engaging with the urban community, saying everyone has a part to play in water quality.
"We are stepping up and doing our bit and throwing rocks at farming all the time is just not helping at all."
Mr Allen said farmers liked clean water as much as anyone did, and needed it just as much, and a straight forward question on this would have produced 100 percent support for clean water, not 82 percent.
He was responding to the survey and comments made to Morning Report this week by Fish and Game chief executive Martin Taylor.
Mr Taylor told Morning Report that local authorities had for too long allowed intensive farms to become established in unsuitable areas, and then protected them at the expense of the environment.
"These survey results show they have the public's support to tackle an issue Kiwis are deeply concerned about."
The survey was done before independent scientific tests for Fish & Game on three Canterbury rivers revealed strains of a severe pathogen which can cause kidney failure and, possibly for the first time, antibiotic resistant E. coli.
Mr Taylor said most farmers were operating within the existing rules and the problem was the rules were too weak - that needed to change.
He said local government should start listening to voters' concerns.