Instances of VTEC, a harmful strain of E. coli, which may lead to kidney failure, have doubled in 2011. Contaminated well water is believed to be a major source, the report stated.
"We are concerned about the growing number of VTEC cases," said Valerie Doyle, senior inspector with the Office of Environmental Enforcement.
"Any form of E. coli is an indicator of fecal matter in the water supply, and VTEC is a harmful form of E. coli. It may cause gastroenteritis, but its toxins can lead to far more serious consequences including kidney failure," Ms Doyle explained.
"We would urge the owners of private supplies to check their water sources. They also get vital information on what to look out for on Local Authority and EPA websites."
The poor weather this summer is believed to have caused serious difficulties for people with wells supplying domestic drinking water.
High levels of rainfall can lead to contaminants being washed into wells as private supplies are less secure than public water supplies.
"We would urge the owners of private wells to test them carefully, given the bad weather we've had," said Ms Doyle.
"Owners should ensure that they are designed, located, installed and maintained properly. Wells should be tested regularly, particularly after a prolonged period of heavy rainfall, since this is when the well may be overwhelmed and become contaminated."
The poor performance of private water sources came against a background of improved public supplies. The EPA's report showed that public water supplies serving more than 80pc of the population had improved year-on-year since 2007.
"The work we have been doing with Local Authorities is paying off," said Gerard O'Leary, director of EPA's Office of Environmental Enforcement.