Federated Farmers dairy head has called a top scientist an eel expert who doesn't like farmers, while the scientist has accused him of talking red herrings.
The row developed on TV ONE's Breakfast after Massey University's Dr Mike Joy called for New Zealand to place a cap on the number of cows in different river catchments.
Joy told the programme dairying is having a hugely negative impact on the country's environment. He said nitrogen inputs into the land have increased by 800% in the last 20 years with farms leaking nitrogen into streams.
He said more than 60% of New Zealand's freshwater fish are on the threatened species list, the pollution has a direct impact and the dairy boom is out of control.
But Federated Farmers dairy chairman Lachlan McKenzie hit back, saying Joy does not like farmers and was just expressing one opinion.
He said even the Prime Minister had said it was only Joy's opinion when interviewed about the scientist's statements on the BBC's Hard Talk programme in London earlier in the year.
Joy had said at the time that New Zealand is delusional about how clean and green it is because species are threatened with extinction and half the country's lakes and 90% of lowland rivers are now classed as polluters.
"The facts are that introduced species have a significant effect both on land and in our aquatic systems, " McKenzie said.
McKenzie held up a report he said shows that algae growth has decreased in rivers monitored between 1999 and 2006 and described Joy as "an expert on eels".
McKenzie said invasive "invasive species" that have been introduced into New Zealand waterways, such as carp in Waikato lakes, have affected the aquatic environment significantly.
He asked Joy: "Which of the universities, schools, hospitals does he want to shut down because 70% of our income comes from primary production. I talk facts, he talks his opinion."
McKenzie accepted that cows walking into streams cause problems but said that's why a massive fencing programme has been introduced under a Clean Streams Accord.
"And that's why the majority of cows now are fenced out of waterways in New Zealand".
But Joy said everything McKenzie had said could be classified as a red herring.
"He's just taking away from the reality. This idea that these invasive species are having some sort of impact is just not true." Joy said, referring to McKenzie's claims about carp degrading waterways.
Joy said the outcomes of the Clean Streams Accord are not measured and the intensification of dairying is what has had the biggest effect on the environment.
"You should think of the Clean Streams Accord as just an education programme. There's no way that that can have the outcomes that will clean up the streams. Every measure of what's happening to our fresh water in New Zealand is showing declines."
Nowhere in New Zealand is there an improvement in fresh waterways, Joy said.