The first major review of RE teaching in 15 years has sidelined the views of non-believers and risks creating "irrelevant" lessons for pupils, secular campaigners have warned.
New guidance fails to give non-religious groups a voice in drawing up RE courses, even though syllabuses are supposed to include their views.
Refusing to fully include secular beliefs contradicts human rights law and risks alienating non-religious students, it has been claimed.
The concerns have been raised following the publication of draft guidance on the way RE is organised. Ministers are expected to publish a final version in the autumn.
There is no national curriculum for RE, meaning syllabuses have to be drawn up in each local authority area. The quality of provision is then monitored by groups called Standing Advisory Councils on Religious Education (Sacre).
Different religions are given places on Sacres. Non-faith organisations had hoped the new guidance would also recommend giving them a voice, but it has not.
"It has failed to come to terms with the massive change in society's non belief," said Keith Porteous Wood, director of the National Secular Society. "RE can't talk about the context of religion without pointing this out, unless what they want is indoctrination.
"Many people on Sacres are pontificating from above and are not in touch with children and classrooms. Giving non-believers a say would make what's taught in schools more relevant."
Mr Porteous Wood is also calling for pupil representatives to be put on Sacres to make RE more tailored to student interests.
Andrew Copson, head of education at the British Humanist Association, also criticised the guidance, describing it as a "big missed opportunity". "They have pulled back from equality," he said. "It is a ridiculous position that humanism should be included in the curriculum, but no humanist need be part of drawing up that curriculum."
Mr Copson said he had expected that the introduction of the Human Rights Act would lead to increased inclusion for humanists. As well as religion, the act protects the rights of other beliefs, including atheism and agnosticism.
Since September 2008, the Qualifications and Curriculum Authority has also advised that secular world views be included in religious education in secondary schools.
The RE review was ordered by the Government at the beginning of last year and followed an Ofsted report that criticised poor lessons and variable teaching quality.
Ministers agreed that the subject's framework needed to be scrutinised and brought up to date. However, the Government shied away from updating more contentious rules that say all schools should hold daily acts of collective Christian worship.
Rev Jan Ainsworth, head of education at the Church of England, criticised the new guidance for failing to uphold the previous guidance that 5 per cent of the timetable should be dedicated to RE.
"We think there is a real danger that RE will get lost," she said. "There is now no obligation to make sure there is enough time for the subject."