Raw sewage is being discharged into rivers and bathing areas at more than 40 locations around the country.
A report published by the Environmental Protection Agency found that 42 areas had no waste water treatment plant which means effluent is entering waterways.
Some of Ireland's main tourist attractions are affected, such as top surfing spot Bundoran in Co Donegal, Cobh in Co Cork and Roundstone in Connemara.
The urban waste water report also found that of the 170 treatment plants in the country, 44 do not comply with EU quality standards, though 94% of Ireland’s urban waste water now gets secondary treatment, three times more than a decade ago.
The EPA's programme manager David Flynn said Ireland's tourist hotspots were being put at risk.
"These areas are ones where people are using the water. It's just unacceptable that raw sewage is still entering the water at this stage," he said.
The agency is calling for more state investment in sewage infrastructure.