The bishops last night disputed claims by Education Minister Batt O'Keeffe that they would relinquish control of up to 1,500 of their primary schools within two to three decades.
The church runs more than 3,000 primary schools across the country, or 92pc of the total figure.
The remainder are run by the Protestant churches, Educate Together, the Irish language movement and others.
The minister yesterday made the surprise statement that the Catholic primary sector may ultimately fall to 50-60pc of overall provision.
He said that this would still allow the church to fulfil its expressed commitment to meet the needs of parents who wished to have a Catholic education for their children.
But church leaders rejected his predictions and challenged him to produce the evidence.
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Bishop Leo O'Reilly, who chairs the Catholic Church's education commission, agreed that there were too many Catholic schools, but said he believed the percentage quoted by Mr O'Keeffe was too low.
And Fr Michael Drumm, executive chairperson of the Catholic Schools Partnership, said that the bishops had not yet seen any research from the Department of Education and Science to support the minister's claim.
"To facilitate parental choice the department must make clear what are the available forms of patronage. Before parents can make a choice they must know what alternatives are available," he added.
Mr O'Keeffe made his contentious comments at a conference yesterday where he also said his department would shortly name 10 urban areas deemed to have too many Catholic schools. Dublin and a number of other large cities will be included, but there will be no small stand-alone rural schools on the list.
Mr O'Keeffe said the decision on which schools should close would ultimately rest with the Catholic Church.
He gave an example of a situation "where there are four or five schools in an area and all of them are Catholic schools".
He added: "Even allowing for 80pc demand for Catholic provision, then it is likely in that area that at least one of the five schools in that parish, or part of a diocese, will not be needed to meet Catholic needs.
"If in the same locality demand from Catholics fell to 60pc, then two of the five schools could be surplus."
He said that after the Catholic community had decided which schools were "surplus", a decision would be taken about who took over the patronage.
The identification of the 10 key areas follows historic discussions between the department and the church last November.
The minister stressed again that stand-alone rural schools would not come under consideration for transfer of patronage. But Mr O'Keeffe suggested "clustering" of small schools under a common board of management and one non-teaching principal.
He rejected calls from the opposition and INTO union that a forum be set up on school governance, saying he did not believe it was needed.
Union general secretary John Carr said the minister appeared to be turning his back on an opportunity to shape future school provision in a planned, coherent and transparent way.
Fine Gael education spokesman Brian Hayes said that many parents would feel that a deal between the Catholic Church and the State had been done behind their backs following Mr O'Keeffe's statement.
"What is needed in the debate on ownership and control of our schools is a public dialogue between all partners in education and, crucially, that the voice of parents is heard," he added.
The restructuring of primary education will be a main issue on the agenda of the three-day spring meeting of the Irish Bishops Conference which begins on Monday at St Patrick's College, Maynooth.
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