Massey University says rural residents are not getting the message about cleaning and testing their tank-supplied drinking water.
The director of Massey's Roof Water Research Centre, Stan Abbott, says hundreds of thousands of rural households drink water that is below minimum standards and is contaminated with fecal pollution.
Bird droppings and dead rodents and frogs are the main sources of contamination, he says.
Mr Abbott says some residents may be immune to the pollutants, but it's likely that a lot of people fail to report gastro-intestinal upsets that have originated from contaminated water.
He says rural residents need to inspect their tanks annually and, if necessary, have them professionally cleaned.