Local authorities have been criticised by the Environmental Protection Agency (EPA) for failing to introduce adequate measures to protect against water pollution in rivers and lakes.
According to one of three reports on water quality being published by the agency today, pollution levels rose in four counties, while more than half of the rivers in a further six counties had levels of phosphorus pollution which breached EU limits.
Overall the three reports revealed that while there has been progress in some areas, Ireland continues to have significant water pollution and contamination problems.
In terms of drinking water, the reports reveal a continuing problem of contamination in small group water schemes, with one quarter of the schemes found to have some level of animal or human waste contamination.
The reports also show that nearly 40 per cent of Irish rivers and lakes fail to comply with quality standards, while in 2001, one quarter of the waste from public sewerage schemes being discharged into lakes, rivers and estuaries was untreated.
Senior scientists with the EPA have said the reports indicated that major investment programmes in water and sewerage schemes have resulted in improvements in water quality in the last four years, and the reports give grounds for "cautious optimism".
The three reports were published simultaneously by the EPA to provide an overall picture of water quality in Ireland.
The most serious ongoing water quality problem was identified in the report on the implementation of phosphorus regulations.
It found the number of totally pollution-free rivers in Ireland has declined from 3.1 per cent to 2.7 percent between 2000 and 2002, which was "a serious cause for concern".
The regulations are designed to reduce the amount of phosphorus, a pollutant resulting mainly from farmyard pollution such as run-off from animal waste.
It is one of the main causes of water pollution in Ireland.
The report found that 38 per cent of rivers and 36 per cent of lakes have levels of phosphorus that exceed limits allowed under EU regulations.
Under the regulations all rivers and lakes are required to be compliant by 2007. According to the report, it will take years for this to happen.
The report also found local authorities have not been using their powers, such as agricultural by-laws, properly to police agricultural activities and to regulate slurry spreading.
It also found that pollution from small industries was "not being properly regulated" by councils. "This is a serious problem that cannot be allowed," according to the report.
The EPA report into drinking water quality found that overall quality had improved steadily between 2000 and 2002.
Overall compliance with drinking water standards stood at 95.9 per cent.
However it found that group water schemes, which serve 8.1 per cent of the population, continued to have a significant problem with faecal coliforms, a measure of contamination from animal or human waste.
A total of 25.9 per cent of group water schemes had some form of faecal contamination in 2002. This was a significant decline on the rate of 32 per cent the previous year.
The third report, on urban waste water discharges, found that 23 per cent of discharges from 412 sewerage schemes were untreated in 2001.
However, because of major ongoing investment, all 412 sewerage schemes are expected to have treatment plants over the next three years.
Dr Matt Crowe, of the EPA, said the reports provided "an overview of water quality in Ireland". "Overall water quality has been improving and that's a reflection of the investment going on in tackling deficiencies in infrastructure".
However, the EPA was concerned about the the decline in water quality in some regions, which was shown in the phosphorus report, which Dr Crowe described as "a big worry".
"Certainly it's going to require a lot of work. Local authorities need to get down to the individual stretches of river and identify the source of pollution in each case.
"It's labour intensive and local authorities will need extra resources. It is not an insurmountable problem and we would be cautiously optimistic that it can be done."