The failures occurred at the Ballymore Eustace water treatment plant and at the Creagh water treatment plant serving Gorey in Co Wexford.
There has been 52 confirmed cases of illness associated with the Gorey outbreak, including bacteria linked to E. coli, with a number of associated hospitalisations.
EPA Director General Laura Burke said there were unacceptable delays in notifying her organisation and the Health Service Executive about the incidents.
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