More than 50 treatment plants supplying drinking water to 1.1 million people are "vulnerable to failure", the Environmental Protection Agency (EPA) has warned.
It says the situation poses 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 solid 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 utility was addressing the deficiencies in the 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.
"Irish Water needs to urgently address the underlying causes for the delays and shortcomings highlighted in this report and prioritise investment to ensure that public supplies are safe and secure, and that public health is protected," she said.
The EPA's annual assessment of public drinking water reviewed 120,000 test results provided by Irish Water.
The fact that 99.9pc of them were within limits for bacteria and 99.6pc of them were within chemical limits did not assuage the EPA's overall concerns about the condition of many plants.
"Regardless of how safe our water is, EPA currently cannot say that it is secure," its report says.
Major issues at the Leixlip water treatment plant, which serves more than 600,000 people, were responsible for a surge in the number of people affected by water quality problems in 2019.
But 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 upgrades or improvements. The number increased to 53 last April.
A total of 67 boil water notices were issued in 16 counties during the year, and there are currently 17 boil water notices in place in nine counties affecting 15,000 people.
Eight water restriction notices, which advise against drinking even after boiling, were also put in place in seven counties, affecting more than 9,000 people.
At the end of 2019, the EPA was investigating 31 supplies, serving 294,000 people, for breaches of pesticide limits.
During the year, 46 supplies in 20 counties failed to meet standards for THM, a chemical by-product of the disinfectant process, at least once.
Ireland faces referral to the European Court of Justice by the end of the summer if progress is not made in resolving the THM issue.
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 that this is a solid base from which to build," he said.
"The report is clear, however, that much more remains to be done. The building, repair and upgrading of Irish Water's water treatment plants, wastewater treatment plants, water and sewer network will require a multi-billion euro investment programme over many years.
"Irish Water is committed to providing a safe and reliable water supply," he added.
The EPA also said the Department of Housing needed to take "a more active role" in tackling the issue of lead pipes in public buildings, saying: "The full extent of this is unknown and there are no comprehensive plans to carry out replacement works."