Victoria University ecologist Mike Joy said it was a wake up call for councils which had been far too permissive in allowing high stocking rates on dairy farms.
It had implications for dairying, with cow urine one of the major contributors to increased nitrate levels, he said.
And he believed the safe nitrate level needed to be urgently reassessed.
"This is a decision the Ministry of Health and central government are going to have to take on board. I mean it's been four decades of [farming] intensification that has been unlimited."
The report's author, Jayne Richards, said nitrate in drinking water was "likely to be a significant contributing factor to colorectal [bowel] cancer rates in New Zealand and may be of a similar significance as the established risk factors of consumption of red meat ... processed meat, lack of physical activity and smoking".
However, the study found it was unlikely to be as significant a risk factor as obesity or heavy drinking.
The numbers potentially affected by higher levels jumped markedly depending on whether private drinking water wells were included, from up to 500,000 to as many as 800,000.
While town supply water was regularly tested by councils, private wells were not.
Without this data, Richards relied on extrapolating out the nitrate results she did have for 2500 private wells to the 600,000 homes using their own water supply.
And it was not simply a case of overlaying a map of high nitrate levels with one for rates of bowel cancer either, as cancer rates were only collected on a DHB-wide basis, rather than across individual cities and towns.
Richards described her work as "preliminary" and urged further study of the matter in New Zealand.
The work had now been handed to the Ministry of Health which had set up a task force to look at the link between nitrates and bowel cancer.
