Some 161,000 people are at risk of crippling illness from a microscopic parasite in drinking water, watchdogs have warned.
The Environmental Protection Agency (EPA) said 25 supplies to homes, schools, hospitals and businesses around the country do not have adequate treatment to kill off the cryptosporidium bug.
Among them are 26,905 people living in and around Letterkenny, Co Donegal where the improvements should have been finished in 2013.
There are another 62,066 people living under the threat of sickness from the parasite in the Killarney and Tralee areas and 19,689 people in Portlaoise, with upgrade works in both areas to be finished in December.
And 12,823 people are drinking inadequately-treated water in parts of Sligo served by the Lough Talt supply.
Overall the EPA said supplies serving more than 700,000 consumers nationwide need treatment plants and pipes improved to protect public safety.
Darragh Page, senior drinking water inspector in the EPA's Office of Environmental Enforcement, said: "Our biggest concern is about these 25 supplies that have inadequate treatment for cryptosporidium.
"There's a possibility that these supplies could end up on a boil water notice and they need to be fixed as soon as possible."
The EPA's review of drinking water quality for 2016 said the number of supplies at risk from cryptosporidium reduced from 37 to 25.
As of this month, 87 supplies were still on the so-called Remedial Action List for work to be carried out to protect tap water standards.
The watchdog said that last year E. coli was detected at least once in three supplies, compared with seven supplies in 2015.
They were Newcastle Hospital in Co Wicklow, Aughclare-Campile in Co Wexford and An Ghraig in Co Kerry. All three issues were resolved within weeks, it said.
The EPA said more than 3,600 people still have to boil water every day in order to have a clean supply to drink.
The worst of those affects 3,427 people in Ballinlough and Loughglynn in Co Roscommon because of issues in treating cryptosporidium.
Some of the other areas of big populations which are under threat from the bug include Millstreet, Co Cork; Creeslough and Glenties-Ardara in Co Donegal; Kenmare, Co Kerry; the Bennettsbridge supply in Co Kilkenny; parts of Carrick-on-Suir; and people in the area of Clonmel-Poulavanogue.
The EPA also used its report on drinking water quality to raise concerns about pesticides, with much of its focus on the presence of MCPAs which are used to kill off rushes on marshy land.
Mr Page said it was a nationwide issue.
"It's really down to the way that pesticides are being used. Very small amounts of these - if an empty container is thrown in or rinsed out at a river - that's enough to contaminate a water supply," the inspector said.
The EPA warned there is no such consistent approach to dealing with pesticide failures.
It also raised concerns about trihalomethanes (THM) - a potential by-product when chlorine is used to treat supplies.
"The number of supplies reporting THM failures remains high, and a consistent national approach must be adopted to ensure that pesticides are prevented from entering our drinking water sources," Mr Page said.
The EPA issued Irish Water with a list of priorities to improve supplies including robust disinfection; adequate removals of organic matter; eliminating lead; and stopping pesticides from entering water sources.