Archbishop Diarmuid Martin said the process was complex and often necessitated amalgamating schools and consolidating resources.
But he also said the process was meeting resistance from politicians who were "throwing spanners in the works" and looking for more consultation.
Members of the Labour Party, he said, were among TDs who had written to him about schools in their own local areas.
Speaking to RTE Radio's 'This Week' programme yesterday, the archbishop said that "everybody is in favour of diversity of patronage in education except when it comes to their own schools, and this was where the process was meeting resistance."
He warned that as a result, the process was taking longer than anybody expected. He also acknowledged the problem of stand-alone schools in small towns was "a difficult one".
The archbishop said "within a decade" he hoped that half of the 500 primary schools under Catholic patronage would be divested. He said in the future there would be a plurality of what people want for their schools and the Catholic Church would run fewer schools.
"People who want their children to go to a school with a non-religious ethos have a constitutional right to that," he said, adding that he wanted to see that the Catholic elements were consolidated in those schools that were clearly Catholic.