The bacteria, often found in slurry, has been washed into the sea in large quantities in recent weeks. The issue is compounded by southerly winds, which are preventing the effluent from escaping the coast.
Swimming has been banned at the beaches, which include Blue Flag centres — Redbarn in Youghal, Garretstown near Kinsale, and Garryvoe near Castlemartyr.
The Front Strand and Claycastle in Youghal, Coolmaine near Kilbrittain, and Oysterhaven are also closed to bathers.
Levels of the bacteria, which can cause serious food poisoning, were found to “far exceed” EU permitted guidelines.
Cork County Council said the closures were introduced as a precautionary measure.
“Due to the heavy rainfall over the last two months, the county council have advised that levels of E.coli at a number of Cork beaches have breached EU mandatory permitted values,” a spokesman said.
“Following consultation with the HSE, public notices have been put in place on the beaches and the next inspection is due next Monday.”
Youghal, which in 2011 lost Blue Flag status on its Front Strand and Claycastle beaches, has no waste water treatment plant.
A local resident John O’Riordan went swimming in Youghal at 7.30am yesterday, before the restrictions were announced.
After lunch, he returned for a swim with his two sons, Sean, 9, and Fionn, 6, to be informed by a lifeguard that bathing was prohibited.
“I’m not presenting with any physical illness but I feel dirty after being told I swam in contaminated water,” said Mr Riordan.
County engineer Noel O’Keeffe said he hoped that a €20m sewage treatment plant for the town would be approved shortly.
“We have put the project out to tender and subject to funding we could start construction early next year,” he said.
Cllr Barbara Murray, the Youghal-based mayor of Co Cork, said it was vital the project got the green light.
However, she conceded that she was resigned to the likelihood that the town would not recover the Blue Flag status on the two beaches for at least another couple of years.