Federated Farmers says it is unfair to assume all intensive dairy farmers are irresponsible and contributing to the pollution of waterways.
Massey University fresh water scientist Mike Joy has called for such farming to be curbed as the only solution to clean up rivers and streams.
Dr Joy is one of the speakers at the New Zealand Freshwater Sciences Society annual conference in Dunedin this week.
He told the conference that so-called best practice farming can't do enough to stop freshwater degradation and the only real solution is to cut back on plans to intensify agriculture.
But Federated Farmers spokesperson Ian Mackenzie says dairy operations have little impact on the environment when good practice is adopted.
He says farmers have taken responsibility for their poor practices in the past and need to be given a chance to change their ways.
The Environmental Defence Society says the Government needs to act on recommendations from the Land and Water Forum that would put limits on intensive farming.
State of waterways 'economic threat'
Dr Joy has been attacked by critics from the Prime Minister down for his internationally reported views on the harm that intensive land use, especially dairy farming, is causing.
But he says the declining quality of New Zealand's waterways is an economic issue rather than an environmental one, because it's undermining the clean green image that the country is trading on.
He says the degradation of waterways will cause the real damage to New Zealand's reputation if nothing is done to reverse it.
Dr Joy says industry bodies with vested interests in agricultural intensification are intentionally suggesting scientists aren't sure how much damage it is causing.
He compared their actions to tobacco companies suggesting scientists don't know if cigarettes damage people's health.