Professor McGettrick fears that many teachers fail to appreciate the political and social context of their work and do not see the Catholic school as a force for ecumenism and growth.
Scotland has made much progress in establishing a liberal democracy, he told the Catholic Headteachers' Association of Primaries in Scotland at its meeting in Dunblane, but Northern Ireland was different.
"This is a culture in which the Unionist and other interests are working in 'cells' and as a direct consequence there are divisive forces which predominate."
Professor McGettrick said it was essential for Scotland to build on the "outward signs of the inward grace which marks the Catholic school".
Denominational schools had to work towards a society of peace, harmony and openness. "These are not conflicting ideas or ideologies. They can and must exist side by side.
"The alternatives to building communities of love and hope will lead to division and bigotry in Scotland."
Catholic schools were not "stand alone" institutions but part of the state system. There was no reason to believe there would be major changes to this position, or in the role of the education faculty in selecting students to be "approved" by the Church.
Returning to a favourite theme, Professor McGettrick insisted that the success of Catholic schools was about much more than "targets and outcomes dictated by external groups who do not see the Catholic dimension of education". Teachers should not be slow to support the formation of young people.
The leader of Scotland's Roman Catholics also warned that many children arriving in primary school know little of God as popular culture changed the ethos of society.
"Teachers can no longer take for granted that children in primary 1 will even know how to bless themselves or say a prayer," Cardinal Thomas Winning said.
Cardinal Winning urged Catholic teachers to discuss what Jesus meant to them, their prayer lives and their experiences of confession and Mass. They should teach children how to pray.
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