First Minister Peter Robinson has called for an end to Government funding of Catholic schools as part of a push towards an integrated education system.
The education of Protestant and Catholics in separate schools in Northern Ireland is a benign form of apartheid, Stormont's First Minister said last night.
Religious segregation at universities would be considered absurd so why should it continue to be tolerated at primary and secondary school level, Peter Robinson added.
While the duplication of services meant wasted money, the DUP leader also questioned the morality of the system.
Mr Robinson has recommended that a commission is set up to examine a way of bringing about integration.
"We cannot hope to move beyond our present community divisions while our young people are educated separately," he said.
In a speech, the First Minister called for change to a set up which currently sees the majority of Protestants educated in the state system with Catholics attending government-funded schools run by the Catholic church. While specially established integrated schools continue to attract pupils, the sector is dwarfed in size compared to the other two traditional systems.
"I believe that future generations will scarcely believe that such division and separation was common for so long," he said in an address to his former council in Castlereagh.
"The reality is that our education system is a benign form of apartheid, which is fundamentally damaging to our society.
"Who among us would think it acceptable that a state or nation would educate its young people by the criteria of race with white schools or black schools? Yet we are prepared to operate a system which separates our children almost entirely on the basis of their religion.
"As a society and administration we are not mere onlookers of this; we are participants and continue to fund schools on this basis. And then we are surprised that we continue to have a divided society.
"The limited number of integrated schools in Northern Ireland do offer a choice but more often than not they join in the competition for funds against the other two main education sectors and in truth will never create the critical mass needed to make a real difference. "
Mr Robinson acknowledged that the system could not be rebuilt quickly.
"I entirely accept that such fundamental change will not happen overnight but that is no excuse for further delay in making a start," he said.
"I know that we will face difficulties in dislodging the vested interests that are so strong in this sector, but I am absolutely convinced that we must.
"I don't in any way object to churches providing and funding schools for those who choose to use them. What I do object to is the state providing and funding church schools.
"The transition must begin and must be carefully planned and programmed. It may take 10 years or longer to address this problem, which dates back many decades, but the real crime would be to accept the status quo for the sake of a quiet life.
"The benefits of such a system are not merely financial but could play a transformative role in changing society in Northern Ireland.
"Consideration should be given to tasking a body or commission to bring forward recommendations for a staged process of integration and produce proposals to deal with some of the knotty issues such as religious education, school assembly devotions and the curriculum. Future generations will not thank us if we fail to address this issue."