Scientists have been told to conduct their debates according to the science - and not the personalities - in a letter sent by the Association of Scientists.

Photo: Supplied / Public Domain

They have received a reminder of the rules after Jaqueline Rowarth from the Environmental Protection Agency and soil scientist Doug Edmeades took part in a radio discussion about whether prominent freshwater ecologist Mike Joy should be labelled an extremist.

The pair appeared on Jamie Mackay's radio show The Country in April as part of a panel discussion entitled: 'Is Dr Mike Joy an extremist or does he have a point?'

Dr Edmeades also wrote an opinion piece titled 'Is Mike Joy a biased scientist?'

A letter from the Association of Scientists addressing the comments went out to all its members over the weekend, including Dr Rowarth and Dr Edmeades.

President Craig Stevens said there had been a lot of concern from members the scientist was being attacked and not the science.

"In this particular area we're talking about freshwater and land use.

"It's an issue that's incredibly important for New Zealand from a number of perspectives.

"We were concerned that some of this was proceeding in the media in a way that was not helpful for getting the facts across."

Dr Joy said he was pleased the association stepped in on the matter but it was frustrating to be called out by people with vested interests.

"We've got really big issues to deal with in this country.

"To be involved in this kind of thing is just classic going right back to what we call 'tobacco science' where you try to undermine the message and the messenger because you want to carry on what you're doing."

He said he was concerned about a global trend of scientific facts being manipulated in the public eye

"We're having marches for science and that kind of thing because of the undermining of science by vested interests.

"It's a reflection of that change... people that are involved in business like this are feeling threatened.

"I'm not sure how far to take it... it's certainly unsettling to see this kind of stuff happening in New Zealand."

Doug Edmeades disagreed.

"That's sensational nonsense to me. It seems to be typical of what we get dished up.

"My motivation in this whole matter is to assist farmers in this area of water quality to understand what the facts and figures are and hence allow them to articulate the appropriate questions to the regional council."

He said the association's letter did not accuse him of doing anything wrong.

Dr Edmeades was adamant Dr Joy's public comments that the intensification of dairy farming is problematic for the country's rivers are not balanced.

"Mike Joy's message seems to be nitrogen is the only problem, cows are the only problem. Get rid of cows, which seems to me to be a bit monolithic."

Dr Joy said that simply was not true.

"If he looks at any of my publications or any of the articles, chapters in the book I've written I talk about all of the impacts on fresh water.

"The bit that he does seem to relate to something is actually wrong."

Jacqueline Rowarth, who last year drew the ire of scientists when she claimed the Waikato River was in the top five cleanest rivers in the world, refused to comment.

The association's letter reminded its members of the Royal Society's Code of Professional Standards and Ethics that say members must try to obtain and present facts and interpretations in an objective and open manner.

The society listens to any complaints about its members before deciding if a penalty is necessary.

Members can be thrown out and have judgements made public, something that the Royal Society said could have a significant negative impact on their career.