Bishop Leo O'Reilly, chair of the church's education commission, said Monday the church had been given no warning of last Friday's announcement by Mr O'Keeffe.
In a speech to Catholic school managers, the minister declared the church 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. But that would fall to about 60pc, said the minister, who did not say how the 60pc figure was arrived at.
Senior church sources said the bishops were angered over a perceived lack of courtesy by the minister and his officials in not giving any warning of the comments last week.
Church officials met the education department last November and officials had undertaken to conduct research in a number of areas before having more talks.
Commenting on the 60pc figure, Bishop O'Reilly said he did not know where the education department got that from.
"It would vary greatly between city and country -- 60pc might be acceptable in Dublin or a large urban area but not in rurals schools," he said.
But Dublin's Archbishop Diarmuid Martin said he had no problem with the numbers being suggested.
He said: "It's not just about buildings. It's about the re-orientation of schools, ethos and the rights of parents and teachers. That will take time and we need to get our research done."
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