Recent European and Scottish legislation emphasises the importance of children's rights but, in an era of continuing decline in church membership, teachers continue to put parents' rights and wishes before those of young people.
Dr Kay Tisdall, policy and research manager, said: "An increasing focus on children's rights suggests that the choices and views of children and young people themselves must be given greater weight and we need to have much more debate about how that can happen."
Dr Tisdall's conclusions follow a small-scale study and two-day seminar, chaired by Lord Clyde, involving a cross-section of vested interests.
Professor Kathleen Marshall, child law expert and visiting Glasgow University lecturer, told the seminar that the 1980 Education Act, which gives parents the right to withdraw children from religious instruction and observance, "sits uneasily" with other stipulations about children's rights.
Professor Marshall said: "How can we in Scotland reconcile a reluctance to ascribe freedom of thought, conscience and religion to children - particularly conscience - wit a system that deems them capable of assuming criminal responsibility at the age of eight?"
Children in Scotland maintains that adults' and children's views of their rights need not be placed in opposition. "Pupil councils and the work of HMI in evaluating current religious education provision may constitute a useful way to the complex question of religious involvement in mainstream education."
Interviews with adults working in children's services confirmed that family and community breakdown and pressures to achieve material success reduced children's chances to develop self-esteem, self-respect and resilience, it says. "Religious moral frameworks and values offered an opportunity to develop these much-needed qualities and skills, even for non-observers."
The study was underpinned by concerns about "the reduction in membership of faith communities". "Religious education was one possible approach to falling participation, particularly for minorities, as it was seen as giving an entitlement to a religious and cultural heritage."
The relationship between religion and services to children in Scotland: research summary and symposium is available from Children in Scotland, price pound;2.50 (Tel: 0131 228 8484).