The government is failing to manage the risk of farming to human health because there is no tool to manage effluent run-off from farms, Fish and Game says.
Tests have confirmed the bug that caused the campylobactor outbreak in Havelock North was from a ruminant animal.
A monitoring tool used by councils to analyse freshwater quality does not measure effluent run-off. Photo: RNZ / Cole Eastham-Farrelly
Seven out of 11 regional councils rely on a software tool called Overseer to manage freshwater quality by analysing farm nutrient run-off.
The system is run by the government, the fertiliser industry and agricultural scientists.
Fish and Game senior regional planner Peter Wilson said there was a significant flaw in that system.
"Because pathogen pathways are not built in to Overseer and Overseer is often the only tool used by regional councils to manage this, we've effectively forgotten an important component in managing our environment."
That missing component was the biggest risk to human health, Mr Wilson said.
"Councils put significant emphasis on [Overseer], but mainly for things such as nitrogen and phospohourus."
The government was taking an "ambulance at the bottom of the cliff" approach, he said.
"There is always monitoring and sampling of rivers and waterways, but that's dealing with the end result of the pollution rather than the source of pollution, so there is an urgent need for pathogens to be built into Overseer."
Overseer chief executive Caroline Read said the software looked at how nutrients in faeces might run off across the topography of the land, but it did not factor in the effect of weather.
"It doesn't consider a heavy rainfall event because it gives a long term estimate of the nutrient losses."
Hawkes Bay received extremely heavy rainfall about 10 days before the outbreak became apparent.
Ms Read confirmed Overseer did not monitor pathogens.
When it was set up 20 years ago the focus was just on nutrients, she said.
"It was looking at how can we account for and how can we understand nutrient losses.
"The conversation wasn't being had about those other human health aspects - that would be obviously talked about in a different conversation."
Overseer was open to discussing the inclusion of pathogen modelling, Ms Read said.