A report by the Environmental Protection Agency has found that water quality in private water supplies is 'consistently' poorer than in public supplies.
Around 20% of the population get drinking water from private water supplies.
The report looks at levels of E coli compliance as an 'important indicator' of water quality.
While the compliance rate in 2015 was 99.9% in public water supplies and 100% in public group schemes, that dropped to 96.1% in private group schemes and 94.8% in small private supplies.
The EPA estimates that up to 30% of the 170,000 household wells in Ireland are contaminated by E. coli through human or animal waste.
According to the report, there has been an increase in cases of VTEC - a pathogenic form of E. coli.
Patients who suffered from a resulting illness are up to four times more likely to have consumed untreated water from wells.
The EPA is urging anyone with a private water supply to check the source of their supplies - including to see whether surface water can get into the well, and if animals can get into a stream or spring.
It also suggests to check for any potential sources of pollution - such as septic tanks or chemical storage.
Gerard O’Leary, Director of the EPA’s Office of Environmental Enforcement, said: “Despite recent improvements to private water supplies, there were 94 private water supplies affecting over 5,400 people on boil water notices.
"Further improvements are required to ensure that people on private water supplies have access to clean and wholesome drinking water.”