"At the moment, I am the patron of almost 90pc of the primary schools in Dublin. That is a relic of history rather than a relic of reality," he said.
However, he added: "That doesn't mean that the Church removes itself from education." He said the choice of parents on their children's education is these days a far more diverse issue.
"There are parents who don't wish their children to have a religious education.
"There are those who want their children to have a religious education as part of a curriculum. They are those who want a robust Catholic ethos for their schools," he said.
"We have to try and canvass and find out what the objective level of support for each of these is and to build a system which will allow for pluralism but which can also be economically viable," he added.
"This requires seeing what parents' desire. It also has to look at teachers -- there is the same diversity amongst teachers and they have a right to be able to teach in a school that fits the model that they have."
The education department has begun surveying parents in 44 areas to establish which patrons they wish to see operating primary schools. The initiative follows an advisory group report recommending the divesting of patronage where there is a stable population and demand for diversity of school types.
Dr Martin said parents would make decisions for future generations.
"I could see in an urban situation that you could well have over a period of time that 'School A' would be moving in the long term toward a more secular model and 'School B' would be Catholic.
"Over a short period of time, you would have different model schools. People would know from the first year on what type of school it is.
"Teachers will also have an opportunity -- while respecting their rights and seniority and so on -- to move from one school to another."
Dr Martin was speaking at a symposium on Catholic Higher Education took place at Mary Immaculate College in Limerick.