Dr Niall Muldoon says admissions based on denomination "just wouldn't stand up in any other area of a child's life"
The Ombudsman for Children says no other European country would allow public school admissions to be based on religion.
Dr Niall Muldoon says the situation is unacceptable, and that Ireland has found itself in contravention of international conventions as a result of the so-called 'baptism barrier'.
Speaking to Newstalk Drive, he argued: "It's something that just wouldn't stand up in any other area of a child's life. If he went to an A&E department and was chosen on the grounds of religion, there'd be uproar about it.
"It doesn't seem to make sense in this situation either, where one of the most important aspects of a child's life is education. Publicly funded schools need to be able take children regardless of the denomination," he added.
Education Minister Richard Bruton has said new legislation will ensure that any school that is not oversubscribed must admit children who apply. 80% of schools are said to be not oversubscribed.
Dr Muldoon said: "Human rights apply to everyone. Over-subscription... the denomination of a child shouldn't come into it - it should not be a consideration for why a child gets into a school or not. It automatically disbars a number of children immediately, and that's inappropriate - that's contravening their rights.
"From our point of view we're very clear that the human rights of every child are important - whether they're of a religious persuasion or none, it's crucial they have the same access to publicly funded schools. Certainly there's options in private funding that's a different situation - but a publicly funded school should provide the service to all children, regardless."
Separately, the Ombudsman has revealed that a 13-year-old boy had to be home-schooled for two years - after applications for access to 28 facilities failed.
The case is highlighted in a report from the office on access to education here.
The report states the boy in question was ultimately "given a school place after two years outside the system and was reported to have been progressing well after a difficult start."
Dr Muldoon says his office has made a "number of submissions to Government on education policy and legislation, including the Education (Admissions) to School Bill 2016".