Catholic educators and humanists alike say they feel marginalised, despite ministerial claims that Curriculum for Excellence marks a new dawn for RME.
One RME teacher at a conference in Edinburgh said her department was being "sidelined" because the interdisciplinary emphasis of CfE meant "everybody's doing it (RME)".
Staffing at her school was being reduced and less of the timetable devoted to the subject, said the teacher, who asked not to be named. Among other explanations offered by senior management was the argument that RME was being put under pressure by the national two-hour PE target, she said.
The wide-ranging concerns emerged at the event despite unequivocal support given by Education Secretary Michael Russell.
There was a "significant and clear place" in schools for both RME and religious observance, and "we have to insist on that". They led to young people who were "tolerant and more understanding, more plugged into the world, and more capable of thought and creativity", Mr Russell told delegates at the event, "Keeping Faith in Schools: getting the balance right".
In contrast to the teacher protesting about the dilution of specialist RME, Mr Russell said the subject would enjoy a more prominent place in education, given its new-found status as one of the eight main elements in Curriculum for Excellence.
Catholic educators said they feared CfE's four capacities would marginalise religious solutions to the world's problems.
CfE has separate outcomes and experiences for religious education in denominational schools. Nevertheless, Michael McGrath, director of the Scottish Catholic Education Service, said CfE in general encouraged young people to "see the world through human eyes alone". He said: "We want to help young people see the world through God's eyes."
Teaching and learning should not be "hidebound to careers and material success", he said, recalling the Pope's recent warning that a "purely utilitarian" approach to education was taking hold in the UK.
The "journey to excellence" - said Mr McGrath in reference to the current HMIE jargon - had, for people of religious faith, a "destination that is for eternity".
An Eco-Schools green flag should not be a "notch on the belt", he explained, but a "sign that you're a Creation-friendly school", having understood the environment as "God's gift to be enjoyed, not exploited".
"Religious illiteracy" was the chief concern of James Conroy, former dean of Glasgow University's education faculty and part of a research team exploring RME teaching in UK schools.
Four recent BBC and Channel 4 programmes about the Pope were among the most glaring examples of such illiteracy because of the way their critical approaches were presented, but day-to-day RME was also highly susceptible, he said.
"There isn't a textbook (on RME) for GCSE or Standard grade in this country that is worth the paper it is printed on," said Professor Conroy. They had "no narrative, no critique", only "lists of things to learn".
RME teachers themselves often displayed religious illiteracy; he advocated higher requirements in the training of specialists to bring about more sophisticated approaches.
He found that educators believed widely that RME "should not be too controversial" - a fundamental problem since "religion has always been subversive". Teachers tended to explain biblical phenomena, such as the parting of the Red Sea, as metaphors and natural occurrences, because they were nervous about the potential controversy of more theological interpretations.
The growth of citizenship education was in direct opposition to religion, Professor Conroy argued, as it was "about eliding the distinctions between people; religion is about what distinguishes people".
RME across the UK was also hampered by low budgets, the research by Professor Conroy's team had found: religious education got less time and resources than other parts of the curriculum. In one school, the annual spend per pupil was 30 pence.
Ken Cunningham, former headteacher of Glasgow's Hillhead High, which has pupils of many faiths, said that bringing about an entirely secular education system would be "the worst thing we could do".
Mr Cunningham, an evangelical Christian, warned delegates not to "proselytise and bore the pants off people", but they should not hide their faith.
"If you don't share it, what's the point in having it?" he asked.
THE HUMANIST SIDE
A group of humanist delegates at last week's conference said pupils should opt in to religious observance - rather than opting out as at present - since about 40 per cent of people did not believe in God.
But the Education Secretary, Michael Russell, made clear he favoured the status quo.
The humanists were also unhappy at not being given a speaker's slot or a stand to share information alongside several other displays of religious materials at the Edinburgh conference.
Jessie McCaffery, a member of the Humanist Society Scotland and former headteacher, was reasonably happy with an assurance from conference organisers MacKay Hannah that the society would feature in a similar event to be organised next year.
But she was less impressed with the explanation that Ken Cunningham represented the secular view at last week's event, since his talk, "The challenges of respecting faith in secondary schools", concentrated largely on his own and others' religious beliefs.
HMIE national RME specialist Patricia Watson dowsed any suggestion that Catholic schools deepened religious divides: in her experience, pupils in denominational schools benefited from high-quality anti-sectarian education.
Michael Rollo, a pastor for the Pentecostal denomination, Assemblies of God, who sits on Falkirk Council's education committee, argued that, far from indoctrinating pupils to religious viewpoints, RME teachers often had no religious faith or were "actively hostile to Christian faith".
- Original headline: RE teachers feel `sidelined' by CfE's cross-curricular emphasis