More than 50 water- treatment plants supplying drinking water to 1.1 million people are "vulnerable to failure", the Environmental Protection Agency (EPA) has warned.
It says there is a health risk and criticises Irish Water for "unacceptable" delays in dealing with it.
The EPA said completion dates for planned works to tackle issues such as cryptosporidium, e-coli and chemical contamination had moved suddenly over the past year from a target of 2021 to 2024 or to dates unknown.
It also said a slowdown in lead pipe replacement meant Irish Water's plan to remove all lead from public supplies by 2026 could take 60 years.
EPA director general Laura Burke was highly critical of the way the water company was addressing the deficiencies in treatment plants.
"The growing uncertainty in Irish Water's planning and delivery of critical improvements to water-treatment plants is undermining confidence in the security of supply of safe drinking water," she said.
"Irish Water needs to urgently address the underlying causes for the delays and shortcomings and prioritise investment to ensure public supplies are safe and secure and that public health is protected."
The EPA's annual assessment of public drinking water reviewed 120,000 test results provided by Irish Water.
The fact 99.9pc of them were within limits for bacteria and 99.6pc within chemical limits did not ease the EPA's overall concerns about the condition of many plants.
"Regardless of how safe our water is, EPA currently cannot say it is secure," the report says.
Major issues at the Leixlip water-treatment plant, which serves more than 600,000 people in Dublin, Kildare and Meath, were responsible for a surge in the number of people affected by water-quality problems in 2019.
There were three separate incidents at the Leixlip plant last year.
In March, a treatment chemical dosing pump failed. In October, a blockage occurred in a chemical dosing line.
In November, heavy rain led to a significant deterioration in quality of the water coming from the Liffey and the plant was unable to cope.
For four days in October and nine in November, consumers had to boil their water because it could not be guaranteed it was fully treated.
"These incidents highlighted serious issues at Leixlip water-treatment plant," the EPA said.
Irish Water has said it will have the problems fixed by December this year.
Residents in Dun Laoghaire served by the Vartry treatment plant at Roundwood are also waiting for a major upgrade to be completed.
The work is expected to be finished by next spring.
However, the EPA found issues with supplies in almost every county and by the end of the year 52 water-treatment plants serving 1.1 million people required significant upgrade or improvements.
The number increased to 53 last April.
Irish Water general manager Eamon Gallen stressed the EPA had found that water quality was high.
"Given the size and scale of the legacy issues and condition of some water-treatment plants, Irish Water is pleased this is a solid base from which to build," he said.
"The report is clear, however, that much more remains to be done."