Fresh water advocates say the Environment Minister Nick Smith is ignoring the real problems by blaming birds for pollution in rivers and lakes.
At Lincoln University's annual environment lecture on Tuesday, Dr Smith said some lakes, such as of Manawatu's Lake Papaitonga, are home to many birds, which pollute the water with E coli.
He said there would need to be a massive bird cull to make these swimmable.
Dr Smith said the government was committed to improving fresh water quality but that people who demanded every fresh water body should be safe to swim in were being unrealistic.
Fish and Game's South Canterbury environmental advisor Scott Pearson said the real issue was pollution caused by agricultural run-off.
"The comments that Nick Smith made around birds are very much a distraction tactic to take away from what is the most obvious issue that's facing water quality in these lakes."
Mr Pearson said a 2014 study of Canterbury high country lakes found that birds accounted for less than 10 percent of pollution.
"The Cawthron Institute did a study on the effect of various land use activites and also birds on those high country lakes.
"The study clearly found that birds only contribute between two and 10 percent of the problem, whereas land use was definitely the major contributer of pollution."
Veterinarian and ecologist, Alison Dewes, said the government needed to do more.
"Part of that is ensuring that we're having our best possible effort at ensuring that our waterways are swimmable, while at the same time, helping our farmers understand what the best mitigations are to put in place to stop the nutrients, the pathogens and sediment making their way to our rivers and lakes."
Dr Smith said he had never stated birds were the biggest problem.
"What I want to make quite plain is that I am certainly not saying - and did not say in the speech - that either our native or introduced birds are the primary challenge that we have around water quality.
"[I am] simply stating the fact that they make it impossible for a rigid rule, requiring every single water body to meet those those swimmable standards."
Dr Smith said there needed to be a pragmatic approach taken to improving fresh water quality.