Environment Minister Phil Hogan has blamed a statistical glitch for some beaches losing their coveted blue flag status.
As eight bathing spots were stripped of the prized status and another eight not even put forward for the award, the minister said the issue would be raised with European chiefs.
An updated grading system has been attacked by Clare County Council after two of its most popular beaches, surfing and tourism spots at Lahinch and White Strand at Miltown Malbay were stripped of their blue flags.
Paul Moroney, the authority's senior engineer, said that a statistical anomaly in testing meant beaches with higher levels of E coli could pass and others could fail for having one bad day.
"Even by the newly introduced Blue Flag standards, which are 2 to 2.5 times more stringent that the previous standards, both Lahinch and White Strand have excellent bathing water, as evidenced in the EPA report on bathing water quality published earlier this month," he said.
"However, a mathematical anomaly that arises when low single figure E coli test results, generally signifying pristine water, are included in the calculations would now appear to have resulted in both bathing waters losing their blue flag status."
Clare County Council said the new analysis regime was not adequately equipped to deal with clean waters and should be reviewed.
An Taisce said other beaches to lose their status included four in the Fingal County Council area of north Dublin - Skerries South, Donabate, Brook at Portrane, and Velvet Strand at Portmarnock - and Ballybunion north beach in Co Kerr, and Ceibh an Spideal in Co Galway.
Applications were not received last year for Dollymount in Dublin city; Redbarn, Garryvoe, Garretstown and Barleycove in Co Cork; Morriscastle, Co Wexford; Bunmahon, Co Waterford, and Old Head in Co Mayo. Mullaghmore in Co Sligo could not be considered because it has a long running issue with livestock roaming on the main beach.
Mr Hogan said he was concerned about the impact of the new grading system which required 95% compliance with water quality standards over four years and that his department would raise the issue with the European Commission.