A majority of local authorities cannot account for more than 40% of the water supply for which they are responsible.
Five city and county councils cannot account for more than 50%.
Minister for the Environment John Gormley has said the findings are unacceptable and urgent action is needed.
This data is contained in what is called the Annual Indicators Report, a document compiled by the Local Authorities for the Environment Minister.
For the first time, the report examines what is termed 'unaccounted for water' - the majority, but not all of which, is down to leaks.
Of 34 city and county councils, 22 could not account for more than 40% of their water supply.
The five which could not account for more than 50% were Cork City, Kilkenny County, Offaly County, Roscommon County and South Tipperary County.
In contrast, the four Dublin local authorities performed well, while the lowest unaccounted rate of 16% came from Limerick County Council.
Minister Gormley has described the rate of water loss as simply unacceptable and warned that local authorities must take urgent action to tackle the problem or risk losing out on funding.
With water charges for households being considered by Government, the fact that so much water cannot be accounted for will make the issue even more controversial.