Minister for Education Mary Hanafin has said she does not expect schools that have already paid water charges to receive a refund.
Speaking on RTÉ's Morning Ireland this morning Ms Hanafin said: "I don't anticipate a situation where Government will be turning around to pay a refund to schools who have always paid water charges and who have paid the same amount each year."
Minister for Education Mary Hanafin
"A lot of schools have paid their bills. There are just some schools that have particular increases that found they were not able to meet those and they are the ones that haven't paid yet.
She went on to suggest that although schools were being advised to hold on to their bills, it was likely that they would to pay a contribution towards the cost of water.
"I don't think it would be very equitable to those who have paid, to suddenly turn around to people who didn't pay for a number of years and say 'you don't have to pay'."
The Minister said there were "obvious problems for schools that have got sudden increases" and that a transition period was being put in place until water meters were installed in all schools.
She added that different rates charged by different local authorities was also an issue to be addressed.
She denied the Government position on the issue of schools paying local authority water bills was unclear following the Government climbdown yesterday when it introduced a two-year exemption.
Mr Ahern told the Dáil yesterday that schools would be required to pay a flat rate charge "appropriate to their size" for a transition period.
Today, Ms Hanafin said the Government was working on scheme which would see a basic threshold given to all schools proportionate to their size and that for water used "over and above that they would have to start to pay".
"We wouldn't anticipate that they [schools] will be holding on to bills for a two-year period . . . [just] until we come back in January with the actual transition scheme.
"We will be looking at the metering and then to make sure schools are putting in place conservation methods."
She said schools that have a particular problem with a leak for which they lack the funding to repair, should forward details to the Department of Education.
Ms Hanafin said the reason Irish schools had to pay water charges while those in France and other EU countries did not was because Ireland did not have domestic water charges.
The controversy over the charges has reopened the debate about primary school capitation grants, which are half the size of those for post-primary schools.
Many schools have paid water charges since 1962, but other schools have paid nothing.