Irish Water is embroiled in a row with local authorities and the Environmental Protection Agency (EPA) over who is responsible for up to 200 small drinking water plants across the country.
The company has failed to comply with three legally-binding directions to upgrade small plants in Galway, Kilkenny and Wexford, claiming the works are the responsibility of the local council.
And the EPA has also confirmed that planned upgrades to plants have failed to improve drinking water quality. In most cases, the projects were inherited by Irish Water from local authorities, and the measures taken did not work.
"The solution put in place didn't fix all of the problems with the supply," EPA senior inspector Darragh Page said.
"Most, if not all [of the projects], were designed by the local authority and given to Irish Water.
"When they were completed, not all worked. It's a legacy issue Irish Water have had to deal with."
The EPA's 2014 Drinking Water report says that water quality remains high across the country but that 6,000 households are drawing their water from 16 at-risk supplies, most of which will be rectified by the end of this year.
This compares with 23,000 households unable to drink their water in 2013.
A boil water notice serving one plant, Aughrim Annacurra in Wicklow, was lifted yesterday.
Irish Water took responsibility for the network from local authorities in 2014, and this is the first drinking water report based on the utility's management of the system.
It shows there are 112 at-risk supplies across the country, compared with 140 at the end of 2013 when the company took control. Of these, 30 lack cryptosporidium treatment.
Of the 955 supplies across the country, 12 failed to remove dangerous bugs, including e-coli and enterococci. Irish Water also notified the EPA of 606 cases where water samples breached quality standards.
The report also says the EPA issued 29 directions last year, up from 16 in 2013, ordering that certain works be carried out. In three cases, Irish Water did not comply, insisting it was not responsible for the plants.
The EPA also said that it wanted "more progress" to ensure that plants are being properly operated.
Irish Water said that it had begun work on 171 Water Safety Plans for supplies serving almost 1.5 million people, which would set out the measures needed to protect water sources and improve quality.
Last night, Irish Water said the EPA had removed four water supplies served by the Stillorgan Reservoir in Dublin from the RAL.
Water from the reservoir had posed a risk of cryptosporidium contamination since 2008 due to inadequate disinfection.