Fee-paying schools receive €96 million a year in supports from the taxpayer but Minister for Education Mary Hanafin has ruled out any change to their funding.
However, the Minister has encouraged parents of children with special needs to begin legal action against schools if they refuse to enrol their children.
Earlier this month, new Department of Education figures - published in The Irish Times - showed special needs provision in Dublin is largely concentrated in State schools within the "free" second-level sector.
The school with the highest level of provision was Newpark Comprehensive in Blackrock.
In an article in The Irish Times this week, its former principal, Derek West pointed to a developing "apartheid" in the education system.
Of the €96 million given to fee-paying schools, about €87 million is for the salaries and allowances of teachers. Fee-paying schools have also received approval for €1.3 million in grants under the department's 2006 summer works scheme. Overall, Ms Hanafin says capital support for fee-paying schools amounts to only about 1.6 per cent of the total capital budget for 1999-2004.
There are 55 fee-charging second-level schools in the State, of which 21 are Protestant.
Ms Hanafin told the Dáil this week that State support for fee-paying schools "has been a long- standing feature of our education system and one continued by successive governments".
On special needs provision, she said some second-level schools did not appear to be doing as much as they could.
"A student may be refused enrolment on the basis of criteria in the school's published enrolment policy . . . but the policy must be legal and cannot involve discrimination against special needs students.
"Some schools seem not to be officially refusing to take students with special needs but rather encouraging parents to apply elsewhere on the basis that another school would better meet their needs. I am very concerned about this practice, particularly given all the extra investment [ in special needs]."
She exhorted parents who believe their child "has unjustly been refused a school place" to appeal under section 29 of the Education Act. Where an appeal is upheld, the Department of Education can direct the school to enrol the student.
Jan O'Sullivan of Labour told the Dáil she was struck by Mr West's article which underlined the case for new regulations to deal with schools involved in discrimination. She asked the Minister: "When are you going to do something as opposed to telling us what you think? Schools won't change their ways until they are forced to do so."
Ms Hanafin said the question of new regulations would be examined when an audit of enrolment policies, now under way, was complete. Earlier this year, she appeared to rule out any sanctions against offending schools.
