Dr Niall Muldoon said it was hugely disappointing that the School Admissions Bill, which was debated in the Dáil today, did not address the issue.
Current legislation allows publicly funded religious run schools to discriminate against children of other faiths or none, by placing them further down on school waiting lists.
The vast majority of schools in Ireland are religious run.
Dr Muldoon said any publicly funded organisation that was receiving money to look after children should have no option but to deal with all children fairly.
He said it was unacceptable that Ireland, as a first world nation, had created such barriers.
Dr Muldoon likened the situation it to a hospital Accident and Emergency department choosing patients to treat on the basis of their religion.
He said if that occurred, there would be serious uproar.
He said it made no sense that a child could be refused a publicly funded school place on the basis of their religion.
Dr Muldoon said the Government had a great opportunity to address this issue and urged the Government to amend the bill at committee stage.