Professor AC Grayling criticised the whole concept of faith schools during a brief visit to the Scottish Parliament yesterday.
Speaking at a meeting in Holyrood for a group of secularists and humanists, the academic said of religious-based education: "The argument against faith-based schools can be summed up in two words – Northern Ireland. Or perhaps one word – Glasgow."
A spokesman for the Catholic Church in Scotland said: "It is unfortunate that Professor Grayling chose to make ill-informed comments about Scottish schools.
"The Universal Declaration of Human Rights gives parents the right to have their children educated in accordance with their beliefs."
He said a "mature" education system would allow multiple faiths rather than a one-size-fits-all model.
However, at Mr Grayling's meeting at Holyrood with secular and humanist representatives there was a confidence that, in time, parents would succeed in removing religious education from schools.
He also claimed religions jumped to the head of the queue when it came to debate on public issues across the UK.
Churches which collectively took in 3% of the population on any regular basis found themselves "at the front of the queue of lobbyists", said Mr Grayling.