Nicky Morgan was speaking in order to clarify the rules, after the High Court found the Government had unlawfully excluded non-religious views from the curriculum.
Last month judges ruled that it was wrong to suggest the content of the new Religious Studies (RS) GCSE could fulfil all of a school's religious education obligations.
British Humanist Association (BHA) said it was keen to ensure that alternative world views were put before pupils at Key Stage 4 level.
As a result, ministers have now dropped plans to take the issue to the Court of Appeal, and have acknowled that the statutory duty of schools does go wider than the RS GCSE.
However, new guidance from the Department for Education insists that non-religious beliefs does 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 too.
The message comes after Prime Minister David Cameron used his Christmas speech to stress his belief that the UK remains a Christian country.
Nicky 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.
"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."
It has also been reported that a source close to the Education Secretary 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."
