Schools must teach that Britain is a mainly Christian country and are still free to prioritise religious teachings over atheism, Nicky Morgan has said.
The Education Secretary has moved to clarify the situation after the High Court found the Government had unlawfully excluded non-religious views from the curriculum.
Judges ruled last month that it had been wrong to suggest the content of the new Religious Studies (RS) GCSE could fulfil all a school's religious education obligations.
The case was hailed by groups such as the British Humanist Association (BHA) as ensuring that alternative world views were put before pupils at Key Stage 4 level.
Ministers have now dropped plans to take the issue to the Court of Appeal, and are acknowledging that the statutory duty of schools does go wider than the RS GCSE.
But new guidance from the Department for Education insists that non-religious beliefs need not be given "equal parity" with religious beliefs.
The guidelines confirm that non-faith schools have to reflect the fact that British religious traditions "are, in the main, Christian", while taking account of the teaching and practices of other prominent religions.
The clarification comes after Prime Minister David Cameron used his Christmas message to stress his belief that the UK remains a Christian country.
Mrs Morgan is said to have been concerned that humanists were using the court ruling to pressure schools into giving non-religious views more prominence.
"This Government is determined to protect schools' freedom to set their own religious studies curriculum, in line with the wishes of parents and the local community," she said.
"The guidance I have issued today makes absolutely clear that the recent judicial review will have no impact on what is currently being taught in religious education.
"I am clear that both faith and non-faith schools are completely entitled to prioritise the teaching of religion and faith over non-religious world views if they wish."
A source close to Mrs Morgan said: "Nicky has had enough of campaign groups using the courts to try and force the teaching of atheism and humanism to kids against parent's wishes.
"That's why she's taking a stand to protect the right of schools to prioritise the teaching of Christianity and other major religions"
But BHA chief executive Andrew Copson said: "All the usual contemporary justifications for the teaching about religions in schools ... logically also apply to the teaching of humanism.
"The High Court ruling in this matter has implications for the school curriculum at all ages and further guidance is urgently needed to bring practice into line with the law."
Rev Nigel Genders, chief education officer for the Church of England said: "There has been confusion about the implications of the High Court judgment and we welcome the publication of this guidance note which clarifies the situation and provides assurance that the judgement does not impact on the content of the new RS GCSE."