At least 52 people fell ill after recent incidents led to unsafe water entering public supplies, officials have said.
One incident happened last month at a plant in Wexford which serves Gorey, while a second failure occurred at Ballymore Eustace which serves large parts of Dublin.
The EPA has sharply criticised the "abject failure" that led to delays in notifying both themselves and the HSE about the issues.
An audit of all the nation's water treatment plants will now be carried out, Minister Darragh O'Brien has said - describing the delay in the incidents being reported to authorities as "completely and utterly unacceptable".
Unsafe drinking water
In the Gorey water treatment plant incident, a power failure and a chlorine pump failure resulted in water leaving the plant and entering the public supply "without the appropriate level of disinfection" for around five days (between August 19th and 24th).
The EPA and HSE weren't told about the incident until August 26th, which the EPA says may have prevented a timely public health intervention.
There's said to have been 52 confirmed cases of illness associated with a 'public health outbreak' in Gorey, including several hospitalisations.
VTEC (a dangerous form of E. coli) bacteria is said to have been involved in some of those illnesses.
Meanwhile, the other incident saw unsafe drinking water leaving the Ballymore Eustace plant - the largest water treatment plant in the country - for up to 10 hours on 20th -21st August, "due to the loss of the Cryptosporidium treatment barrier compounded by inadequate disinfection".
Officials in the HSE and EPA weren't told about that incident until September 1st, over a week later - with the EPA again saying this led to a delayed response to the incident.
In a statement, the EPA said there had been an "abject failure of managerial oversight, operational control and responsiveness" by both Irish Water and local authorities.
The agency said: "In both cases the affected consumers were left unaware of the risks they faced and did not have the opportunity to protect themselves, and in the case of Gorey serious illness was detected in the community.
"While Irish Water has the primary responsibility for the safety of the water supply, the failure to report incidents between the Local Authorities and Irish Water prevented a timely risk assessment of the incidents and resulted in unacceptable delays in notifying the EPA and HSE.
"These unacceptable delays in reporting and in particular the failure to consult with the HSE as to the risk to public health during the incidents, meant that there was no opportunity to issue boil water notices to approx. 900,000 consumers of both supplies, which would have served to protect public health until issues at the plants were resolved satisfactorily."
Local Government Minister Darragh O'Brien says the incidents and delays in reporting have left him "furious".
He said: "It's completely and utterly unacceptable."
The minister met with Irish Water and Dublin and Wexford local authorities this morning.
Irish Water is to undertake an audit of the water treatment plants across the country, while "re-fresher training" on incident reporting for all plants will also be arranged.
Minister O'Brien said: “Ultimately, as we all know, there are limitations to the current working arrangements between Irish Water and Local Authorities and it is impacting on the delivery of services.
"A process is underway in the Workplace Relations Commission (WRC) to deliver the transformation of this service but I am also requesting that Irish Water and local authorities to take further steps to improve Irish Water control of all water service plants in the immediate term pending the implementation of the agreed longer term operational and staffing arrangements."