The Department for Education (DfE) is branding a report by the British Humanist Association (BHA) "inaccurate", adding it has "no official status".
A spokesperson for the DfE said: "We have issued clear guidance for all schools. This guidance remains correct. We are clear that the British Humanist Association document has no official status and is inaccurate."
The DfE was speaking after the BHA warned that government guidance risks promoting illegal RE classes by going against a ruling by the High Court last year that religious and non-religious worldviews must receive equal treatment.
An "urgent" letter by the BHA has been written to Secretary of State for Education, Nicky Morgan, calling for an explanation of the Government's position on the issue.
It is accusing the Government of unfairly attacking teacher guidelines distributed by the BHA last month which - it claims - sought to explain the implications of the High Court ruling for RE syllabuses.
The High Court case ruled in favour of three humanist parents who challenged the way non-religious worldviews were covered in the syllabus for GCSE Religious Studies.
BHA Chief Executive Andrew Copson said: "We have asked the Government three simple questions. On what grounds is it saying that it is not for us to publish guidance on this matter? How is the guidance inaccurate? And how can it possibly have concluded that the [High Court's] judgement does not have a broader impact on the RE curriculum?
"Last year's High Court judgement was clear that in order for RE to meet the legal need for neutrality, impartiality, and pluralism, non-religious worldviews must be afforded equal respect to religions in the curriculum.
"In declaring otherwise, the Government risks encouraging schools and others to act unlawfully, and schools and others responsible for RE who rely on the DfE perspective in this matter are relying on the same perspective that led to the DfE being defeated in court last year."