Evangelical Christian groups intent on converting pupils are being allowed into state schools claims a report.
The National Secular Society (NSS) says some groups are holding assemblies and bible clubs in schools in England.
The NSS has written to the Education Secretary Michael Gove calling for national guidance on external visitors, particularly from religious groups.
The government said it had not seen any evidence to support the claims and had not received any complaints.
The report says there has been "a marked increase in the number of parents contacting the National Secular Society with concerns about external visitors to schools exposing their children to unwelcome and wholly inappropriate religious evangelism and proselytisation".
It added: "We have investigated this and found an abundance of material showing that the parents' concerns were not isolated instances."
The report says that in many cases, evangelical Christian organisations offer to provide religious education and school worship.
It claims that the legal obligation on schools to provide religious education and a daily act of worship has provided "a foot in the door" to some organisations with evangelistic intentions.
The report suggests that shortfalls in religious education provision, recently highlighted in a report from Ofsted, are leading head teachers to accept help from external religious groups and adds that some heads are "insufficiently discerning about the external groups they are allowing into their schools".
The letter also asks the Department for Education to ensure that guidance to schools on visits from religious groups "makes clear that schools must not offer opportunities to groups seeking to evangelise".
The NSS says its investigation was prompted after it was contacted by parents, some of whom had themselves written to the schools and to the Department for Education about their concerns.
One parent said he had become aware "quite by chance" of regular visits by an evangelical group to his child's non-religious primary school in Sheffield.
He complains that the group "adheres to a profoundly conservative and avowedly missionary agenda".
Another complained that his child had been told the creation story from Genesis was "factual" during visits to a primary school in the West Midlands from a local minister.
Russell Hobby, general secretary of the National Association of Head Teachers, said: "Religious education must be clearly delineated as such.
"A line is crossed when religious positions such as creationism are taught as scientific theories for example. Neither are schools places for proselytisation without the explicit and informed consent of parents."
A spokeswoman for the DfE said if parents had concerns about visitors to their child's school they should make a formal complaint to the school.
"State schools cannot teach creationism as scientific fact," added the spokeswoman.
"They must offer a broad and balanced curriculum and meet their obligations under equalities legislation. Schools have a responsibility under law to ensure children are insulated from political activity and campaigning.
"Schools are required to safeguard the spiritual, moral, social and cultural development of pupils.
"Ofsted inspections include a focus on this to enable them to identify any inappropriate practice."
Paul Bate of the Association of Christian Teachers and a former head of a faith school said: "Some schools, including faith schools, have a clear statement in their articles prohibiting staff from proselytising within the school.
"Indeed, the faith school where I was head had such a statement within their articles and the RE curriculum was based around the teaching of philosophy, ethics, and giving the students an understanding of all faiths - which included secularism."