The new rules state that from 2013, all free schools in England must teach evolution as a "comprehensive and coherent scientific theory". The move follows concerns that free schools run by creationists might avoid teaching evolution. Sir Paul Nurse, president of the Royal Society, said he was "delighted".
Sir Paul told BBC News the previous rules on free schools and the teaching of evolution versus creationism had been "not tight enough".
He said that although the previous rules had confined creationism to religious education lessons, "the Royal Society identified a potential issue that schools could have avoided teaching evolution by natural selection in science lessons or dealt with it in a such a perfunctory way, that the main experience for students was the creationist myth".
So far 79 free schools have opened in England with 118 more due to open in 2013 and beyond. They are funded directly by central government but unlike other state-funded schools are run by groups of parents, teachers, charities and religious groups and do not have to abide by the national curriculum.
The new rules mean if a free school is found to be acting in breach of its funding agreement - for example, teaching creationism as a scientific fact or not teaching evolution - the Department for Education will take "swift action which could result in the termination of that funding agreement".