Scottish Conservative justice spokesperson John Lamont has said the west of Scotland school system contributes to the "conditioning of sectarian attitudes".
Mr Lamont's comments have produced a furious backlash from the Catholic Church, but television interviews in the region indicated that a significant number of ordinary people share his worries.
The remarks came as Scottish MSPs debated emergency laws to increase jail terms for sectarian-related behaviour connected to football - persuading first minister Alex Salmond that it would be sensible to allow further time to consider the nature and impact of legislation in this area.
Mr Lamont said that segregating children in Catholic and non-denominational schools contributed to the problem of sectarianism and lack of community cohesion.
Speaking from first-hand experience of growing up and attending a non-denominational school in Kilwinning, North Ayrshire, Mr Lamont said tensions with a local Catholic school resulted in pupils spitting and throwing stones and eggs at school buses.
Turning to the bill to outlaw sectarianism in sport, he said: "The reality is that young men who are at these football matches are acting in a way that is a result of the conditioning that is started at a very early age.
"I would argue that certain parts of society, admittedly small, in west Scotland have promoted the culture, including partly through our education system. This segregation of our young people has brought them up to believe that the two communities should be kept separate."
The education system of west central Scotland has "produced many, if not all, of those who are responsible for the shocking behaviour which we have witnessed in recent months", said the MSP for Ettrick, Roxburgh and Berwickshire. "[It] is effectively the state-sponsored conditioning of these sectarian attitudes."
He went on: "I say this as someone who believes, as a Christian country, we should do more to promote Christian values in our young people and support religious education in schools. Clearly these attitudes are being entrenched at home and the wider community in these small pockets of west central Scotland."
The Catholic Church has branded his remarks "offensive" and "malicious".
Community Safety minister Roseanna Cunningham also attacked Mr Lamont's "astonishing diatribe".
The Catholic Bishop of Motherwell, the Rt Rev Joseph Devine, said evidence pointed to an overwhelming majority of Catholic parents, as well as many parents of other denominations, choosing to send their children to Catholic, rather than non-denominational, schools, reports the BBC.
"The claim that Catholic schools are the cause of sectarianism is offensive and untenable," said the bishop, also president of the Catholic Education Commission. "There has never been any evidence produced by those hostile to Catholicism to support such a malicious misrepresentation. Is Mr Lamont really claiming that he knows better than parents what is in the best interests of their children? Is it arrogance or ignorance on his part?"
Simon Barrow, co-director of the Christian thinktank Ekklesia, which promotes community schooling and the reform of faith schools, commented: "This war of words indicates that we need a more rational debate about the short- and long-term impact of religious selection and segregation in schooling in Scotland, as in other parts of Britain and Ireland.
"There is well-researched evidence in the UK, including the Cantle Report, which suggests that separating or selecting pupils on the basis of religion can contribute towards lack of cohesion, lack of real contact between children from different communities, and in some cases the kind of lack of empathy or antipathy that contributes towards direct conflict," said Barrow.
"This is a legitimate concern to raise in Scotland too, and a debate about the kind of state-supported schooling needed to break down sectarian attitudes should not be turned into a 'taboo' by accusatory denunciations directed towards anyone who suggests there is an issue here. The Conservative justice spokesperson may or may not have used what others would regard as judicious language in parts of his speech - but his preparedness to name a difficult issue openly is surely courageous and necessary.
"If Mr Lamont's critics believe that there is insufficient verified evidence on the issue of the relation between religiously segregated schooling and lack of community cohesion or sectarian attitudes, then that suggests the need for more research, not the silencing of the concern," said the Ekklesia co-director.
Ekklesia is a founding member of the Accord Coalition, which works for the reform of faith schools to ensure full equality and inclusion, and for an end to religious selection and discrimination in all publicly funded schools.