The head of the Catholic Principals Association in Northern Ireland has accused the first minister of rabble rousing.
Dr Seamus Quinn said Peter Robinson's words were "a throwback to the bad old days of religious intolerance".
It followed Mr Robinson's comments that the NI education system was "a benign form of apartheid".
The Vatican Radio website picked up on the story with the headline "NI leader against Catholic schools".
On Friday Mr Robinson said that while he had no objection to church schools, he objected to the state funding them.
But Dr Quinn, chairman of the Catholic Principals Association (CPA) said: "The fundamental right of parents to seek a faith-based education for their child must be acknowledged.
"The first minister's recent utterances, marking the appointment of a DUP mayor, appear to seek the removal of this parental right.
"Mr Robinson should be well aware why Northern Ireland has a Catholic-managed system, the Northern Ireland state having singularly failed to provide for its Catholic population from inception."
Dr Quinn said the Catholic authorities had, for many years, provided a network of schools paid for and run by the Church with minimum state support.
"Students from these successful Catholic schools challenged the blatant social injustices facing the minority population and have, in no small measure, transformed Northern Ireland," he said.
"It was as late as the 1990s before Catholic schools finally achieved parity of funding with state schools.
"However, the years of chronic under-investment by the state in Catholic schools has yet to be fully addressed."
At the weekend, Deputy First Minister Martin McGuinness said Mr Robinson was making a mistake.
"If Peter thinks taking on the Catholic Church, the Catholic bishops and indeed the Protestant churches for that matter and other interest groups is a sensible route to go, I think that is a big mistake," he said.
"I think what we have to do is try and achieve and continue to build a consensus within our society about the need to develop shared services.
"If you go for a head-on collision with the so-called vested interests, that is a collision course which will lead us into a total and absolute mess."
On Friday, speaking at the installation of a DUP mayor in Castlereagh, Mr Robinson also said he wanted to set up a commission to look at the total integration of the different sectors.
He compared the system to South Africa during apartheid where black and white children were educated separately.
In an apparent reference to Catholic schools, he said he had no objection to church schools but he did object to the state paying for them.
"It may take ten 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," he said.
"The benefits of such a system are not merely financial but could play a transformative role in changing society in Northern Ireland."
He added that there were a number of "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," the DUP leader said.
It would be difficult to dislodge "vested interests", he said, but was "convinced" that it should be done.
The DUP position has been that the state - or controlled - sector was non-denominational and could be used by those of all religions and none.
Mr Robinson said he was proposing a single education system, rather than enlarging the integrated system which he did not believe would create the critical mass needed to make a real difference.
Noreen Campbell from the NI Council for Integrated Education said Mr Robinson's speech was a significant contribution to the debate on the future of education in Northern Ireland.
"The fact of the matter is that more than 90% of our children are educated separately," she said.
"They are educated separately from the age of three to the age of 18 or 19. That is not an acceptable situation in a divided society when it is looking to a better future.
"I welcome Peter Robinson's intervention. I welcome the debate."