Up to 5,000 schools were sent the packs of teaching materials by Truth in Science, a group of academics and clergy, to promote "intelligent design", an off-shoot of creationism, as part of the science curriculum.
The packs include lesson plans and DVDs, which the group believe will help balance science lessons by questioning Darwin's theory of evolution.
Following complaints from the British Humanist Association and the Christian think-tank Ekklesia, the DfES and the Qualifications and Curriculum Authority will distance themselves from the material and tell schools that it does not form part of the national curriculum. A letter from the DfES to the humanists said: "The department has received a range of correspondence about the teaching of creationism and intelligent design in theJscience curriculum, and about the resource pack sent out by the Truth in Science organisation.
"The national curriculum for science clearly sets down that pupils should be taught that the fossil record is evidence for evolution."
Truth in Science claims that popular textbooks give little coverage to alternative theories to Darwinism. It cites a line in the national curriculum about teaching scientific controversies.
Andy McIntosh, a professor of thermodynamics at Leeds university and one of the five-man board of the group, said: "We are not saying people should not be taught evolution. But there is an alternative way of looking at the data. To say that intelligent design must be put to one side because it is religious is failing to realise that the traditional approach is equally philosophical and religious."
Truth in Science has also caused controversy by its link to the Emmanuel Schools Foundation, which has been criticised for including creationism in science lessons. Steve Layfield, the head of science at Emmanuel College, one of the foundation's schools, is also a director of Truth in Science.
Simon Barrow, co-director of Ekklesia, said: "What is taught in science lessons should be proven scientific theories.
"Creationism and intelligent design are not that. They are bad theology based on inadequate reading of texts. They have nothing to do with science."