The government's nutrient-loss monitoring tool for farms needs to account for runoff that could contaminate waterways, a veterinarian says.
More than 4000 people in Havelock North have suffered from gastric illness following the contamination of the water supply and 523 have been confirmed as due to campylobacter.
Tests have confirmed that the bug was from a ruminant animal.
Overseer is a government tool which is used by seven regional councils to calculate nutrients levels on farms - such as nitrate and phosphorus.
Waikato veterinarian and ecologist, Alison Dewes, said she was worried that Overseer based its work on the assumption that farms were being managed so that no runoff could get into the waterways.
"It assumes that all effluent ponds are fully sealed, it assumes there is no separate run off from crops or tracks or feedlot situations through to connecting waterways or shallow aquifers.
"That mere assumption is giving us a false sense of security around how well some of these farm systems are being managed, and that's an issue.
"That means that we need to go back to the drawing board and make sure we've really got those high-risk points on farm covered."
Overseer also assumed that pathogens were not connecting through or across soil to receiving waterways, which was is incorrect, Dr Dewes said.
Overseer Ltd said it did not model any faecal contaminants and it assumed that farms were being managed with no runoff into waterways.
It said Overseer results should be considered alongside other farm information to get a full picture of the risks.