Raw sewage is being discharged into rivers, lakes and the sea in 42 towns and villages around the State, according to the Environmental Protection Agency.
The material is being discharged despite a European Union directive issued 23 years ago stating that untreated sewage should not be discharged into the water system.
According to the report 94 per cent of urban waste water is subject to secondary treatment, the minimum level required.
However, it found that even where they exist 30 per cent of secondary treatment plants do not meet the required standards.
Seven large towns; Killybegs in Co Donegal; Clifden in Co Galway; Youghal, Cobh, Passage West and Ringaskiddy in Co Cork and Arklow in Co Wicklow do not have secondary treatment plants.
In three of these towns; Ringaskiddy, Killybegs and Arklow the treatment plants are 13 years overdue.
The EPA said more money needs to be invested to eliminate the problem of raw sewage and to protect rivers and beaches and to protect industries dependant on clean water such as tourism and angling.
Gerard O’Leary, director of environmental enforcement, said while progress has been made the release of raw sewerage “needs to be eliminated”.