Federated Farmers has questioned the value of the water quality review by the Office of the Auditor-General because of of the areas it doesn't cover.
The report looks at how effectively four regional councils - Waikato, Taranaki, Manawatu-Whanganui and Southland - are managing water quality.
In addition, it raises concerns about the deterioration in some parts of the country, especially lowland areas that are mainly used for farming.
The Auditor-General concludes that Waikato and Southland regional councils are not adequately managing the causes of discharges, where significant intensification of land use from dairy farming has meant more pressure on freshwater quality.
It says Manawatu Regional Council is keeping up water quality standards in the Rangitikei and Whanganui River catchments, but not for the Manawatu River.
It gives Taranaki Regional Council the best write-up, saying overall it is maintaining and, in places, improving water quality.
Federated Farmers' president Bruce Wills says the report is imbalanced, because it doesn't consider the impact on water quality of point-source discharges from the likes of sewerage systems and processing plants.
Mr Wills says the review is another instance of farmers receiving the lion's share of the blame for poor water quality.
"The farming community's more than happy to put their hand up and say of course we have an impact on water," he says. "But there's been an enormous amount of work over a long, long period of time now to try and mitigate and make progress with being able to both intensively farm and achieve the clean water parameters that we're all keen to get to."
Waikato Regional Council, one of the most heavily criticised in the review, also makes the point that it is well advanced in dealing with the water quality issues raised.
Environment Minister Nick Smith agrees that it's not just farmers that need to be held accountable.
He says the Palmerston North City Council's failure to comply with conditions for discharging waste water into the Manawatu River from its sewage treatment plant is a case in point.