Two-thirds of primary schools are now "in the red" as the financial squeeze worsens, school managers say.
The loss of a grant for minor works has pushed more schools over the edge, according to the Catholic Primary School Managers Association (CPSMA).
The grant was often seen as a cash float in schools while they awaited funding for running costs – which are paid twice a year.
It was worth between €5,000 and €12,000 to many schools and in the 2011/12 year, the last in which it was paid, the total payout was €28m.
The withdrawal of the Minor Works Scheme came on top of the loss of the Summer Works Scheme and cuts in capitation grants.
The CPSMA represents about 90pc of primary schools and vice-chairperson Fr Denis McNelis raised the issue with Education Minister Ruairi Quinn at the association's annual conference yesterday.
He said a five-teacher school with 100 pupils and five with special educational needs had lost a staggering €10,435, which represented 20pc of its funding, as a result of cuts in capitation.
"What start can we provide for pupils on less than 50 cent per day?" he asked.
Fr McNelis called on Mr Quinn to restore the grant as a matter of urgency.
He said parents could no longer contribute as they suffered a serious drop in living standards too.
Mr Quinn said he had to prioritise funding for the provision of school accommodation to cater for growing enrolments.