Federated Farmers says a new Government agency would be no more effective than regional councils in protecting the water quality of rivers.
The Conservation Authority has recommended a Government-controlled agency should take over river protection.
The recommendation is one of 19 put forward by the agency after an 18-month study into the state of rivers under current legislation.
Conservation Authority chairperson Kay Booth says councils and government departments have been ignoring the need for river protection, and water quality has worsened.
She says appointing a government or quasi-government agency specifically responsible for river protection could reverse the trend.
However, Federated Farmers' water spokesperson Ian Mackenzie says that's an over-reaction.
He says he's not sure that this report's recommendation for a new government agency is necessarily the right one when there are plenty of other organisations involved already.
Mr Mackenzie says there's sense in having a standard protocol for water quality markers.