The Government has been accused of irresponsibly claiming that EU regulations mean schools cannot be exempt from water charges.
Bills of up to €10,000 from local authorities for water usage have begun arriving at schools.
Taoiseach Bertie Ahern and Minister for Education Mary Hanafin insist the Government is powerless to block the charges because of the EU water framework directive, which aims to preserve increasingly scarce water resources.
But Fine Gael and Labour said blaming the EU for the contentious charge was particularly irresponsible considering the Government was soon to unveil a campaign urging the public to support a new EU treaty.
Ms Hanafin said today that she had been urging the Department of the Environment to agree to an allowance or threshold below which schools would not be charged.
She told RTÉ radio that when the directive was negotiated in 1999 Ireland had sought a derogation from applying charges for schools and homes.
In what became known in Brussels as "the Irish clause", it was agreed that domestic charges could be waived. "But we didn't win the argument for the schools which unfortunately is why they are being levied," Ms Hanafin said.
However, The Irish Timesthis morning reported a senior European Commission official saying Ireland was entitled under the terms of the derogation it negotiated from the directive to waive a charge to schools.
"I do not really see schools having a serious impact on the purposes of the directive . . . I don't see, really, that this is so much of an issue," Jorge Rodríguez Romero of the environment directorate general said.
Labour education spokesman Ruairí Quinn said the Government was hiding behind the European Commission.
"Not only is it dishonest in itself, according to reports from the EU Commission, but it also fuels the kind of prejudice that will strengthen the No vote in the forthcoming Lisbon Treaty referendum campaign," Mr Quinn said.
He called for the withdrawal of the water charges and a conservation programme for schools to help them reduce water usage.
Fine Gael MEP Mairead McGuinness said the Government's attempt to blame the EU "beggars belief given that the Irish Government participated in the negotiation of this piece of legislation".