The Department for Education has said Michael Gove is "crystal clear that teaching creationism is at odds with scientific fact" after a warning that the government's new free schools could be exploited by fundamentalist churches looking to promote a literal interpretation of the Bible.

The remarks follow a letter to the education secretary from the British Centre for Science Education (BCSE) suggesting that creationists planned to use government legislation on free schools to mount a "concerted attack" on science education.

Free schools can be set up by charities, universities, businesses, educational groups, teachers and groups of parents. They will have more freedom over the contents of their curriculum, leading to fears that science teaching in the schools may not be as rigorous. Teachers working at free schools will also not need to have formal teaching qualifications.

The BCSE, which describes itself as the leading anti-creationist organisation in Europe, wrote to Gove to express its "extreme concern" at applications from groups such as the Everyday Champions Church and the Christian Schools Trust to run free schools.

The Everyday Champions Church, in Newark, Nottinghamshire, submitted its proposal for a 652-place school in January, shortly before the DfE held its first free school conference where Gove said he would consider applications from creationist groups on a case-by-case basis.

On its website the church says it has "660 children 'definitely' signed up to the school and 185 considering". It spent January and February carrying out public presentations and found parental response "overwhelmingly positive".

"Creationism will be embodied as a belief at Everyday Champions Academy, but will not be taught in the sciences," said its leader Gareth Morgan. "Similarly, evolution will be taught as a theory. We believe children should have a broad knowledge of all theories in order that they can make informed choice."

The DfE spokesman said groups setting up new free schools in the UK will be vetted to ensure that they have "strong education aims" and "high curriculum standards". He said: "The education secretary is crystal clear that teaching creationism is at odds with scientific fact. Ministers have said they will not accept any proposal where there are concerns about the people behind the project."

In the letter from the BCSE, Professor Paul Braterman wrote that the embodiment of creationism "as a belief" could only mean that science was "subordinate to religious considerations, and that the central concepts of the natural sciences, as developed over the past 350 years, must be rejected as doctrinally unsound."

In an accompanying report, the BCSE recommended the DfE "carefully vet" free school applications and "be very wary" of approving applications from creationist groups.

Last July, Gove acknowledged there were concerns about "inappropriate faith groups using this legislation to push their own agenda." The education secretary, who was addressing MPs on the cross-party Commons education committee, said his department was working on the regulations to ensure there were no "extremist groups taking over schools".

Braterman claimed that teaching in schools run by such groups in Sweden forced a revision of the original "friskolor" legislation there, making free schools subject to the same regulations that ensure teaching is objective as traditional schools.

• This article was amended on 23 March 2011 to remove a reference to a primary school in Hampstead that has asked us to make clear they have no connection with the Christian Schools Trust.