Edinburgh Secular Society (ESS) has compiled a dossier of activities which it says shows how religion has become "pervasive" within non-denominational state schools. Among the cases cited are fundamentalist evangelical groups pushing ideas such as faith healing and speaking in tongues. Scotland's teaching union, the EIS, said it was concerned by the developments.
The ESS - which supports religious education but wants religious observance taken out of schools - claims there is a lack of monitoring of the activities of evangelical groups in schools and has accused them of "proselytising", and trying to convert children to Christianity.
Gary McLelland, chairman of the ESS, argued there was a "concerted effort" by various Christian organisations to try to "infiltrate" schools.
He said: "We are all in favour of having, for example, pastoral helpers and counsellors, as school is a hard time, especially for teenagers. But the predominantly Christian groups in Scottish schools show a level of organisation and detail that does worry me.
"I don't think it is beyond the pale to interpret this as an attempt by churches to address the issue of falling membership by trying to get in as [people] young as possible."
The ESS dossier comes at a time of growing debate over the issue of religious observance in non-denominational schools in Scotland.
Earlier this month, a petition was presented to MSPs by Secular Scotland and parent Mark Gordon calling for a change in the law, so that parents are asked to opt in before their children take part in religious observance rather than having to opt out, as at present.
Education chiefs also launched an investigation after it emerged that members of an American pro-creationist Christian religious sect, the West Mains Church of Christ, had been working as classroom assistants for eight years at Kirktonholme Primary in East Kilbride.
The ESS said this example has highlighted "woolly guidelines" from the Scottish Government.
McLelland said: "If a religious group wants into a school, they can look up guidelines and say, 'We will fulfil your need for community activities' … They use these kind of weird open-door policies to get access to schools and as we have seen from the example in East Kilbride, the results can be scary."
Among other examples noted in the ESS dossier is the involvement in schools by evangelical group, Scripture Union (SU). As well as running SU clubs, volunteers help out in classrooms. Outdoor adventure centres run by Christian groups which offer schools residential trips are also highlighted, with the report saying it is "far from clear if parents and pupils are being made aware of the evangelical nature of the courses".
For example, in its school handbook, Dean Park Primary in Edinburgh describes an annual trip to an adventure centre run by the Abernethy Trust - affiliated to the Evangelical Alliance - as a "highlight of school life" for P6 pupils.
Edinburgh City Council said parents are informed it is a Christian adventure centre ahead of the trip, and are told that each evening there is a "short Christian presentation" for the pupils, which is not obligatory and alternative arrangements can be provided for anyone who opts out.
The ESS report also raised concerns about the organisation Prayer Spaces in Schools (PSIS). PSIS says it provides activities which help students "consider their beliefs and behaviours".
But the ESS report highlights quotes from the organisation's website from pupils following a prayer space in a Scottish school: "I now believe in God," said one. Another pupil said: "I would now consider praying."
It also notes that PSIS is an initiative of charity 24/7 Prayer International, which has a video on its website claiming that faith healing sessions for conditions such as eczema and Crohn's disease has taken place in prayer spaces.
The ESS also highlighted the expansion of volunteer school chaplaincy teams, with some schools having as many as 10 members. The report raised concerns about members of evangelical groups being appointed to school chaplaincy roles - for example, from Pentecostal churches which promote belief in speaking in tongues.
Secularists have also raised concerns about the number of evangelical volunteers helping out on the sports field.
However, the Christian groups named in the report - which all said any members who go into schools are vetted with criminal background checks - strongly refute the allegation that such moves are about proselytising.
The Church of Scotland said it was committed to the maintenance of non-denominational schools and "has no desire to create state-funded faith schools".
Rev Sandy Fraser, convener of the Church of Scotland's education committee, said: "We are not trying to convert [children] to any faith, we are not proselytising - what we are doing is going in and trying to raise their spiritual awareness."
Andy Bathgate, chief executive of SU Scotland, said staff and volunteers could respond to requests from schools for assistance in activities such as school trips and sports days, reading, breakfast clubs, providing music or administration.
He said: "These kinds of requests come commonly from schools and it is open to any responsible adult to help in this way. The work we do in the area of religious observance gives young people the chance to reflect upon the spiritual dimension to life, an opportunity not afforded elsewhere in the curriculum.
"We agree with the Edinburgh Secular Society that proselytising within a school context is wholly inappropriate. We strongly refute the idea that our work involves exerting pressure, indoctrination or any underhand methods."
A statement from PSIS said its activities helped students develop greater self-awareness, consider moral issues and explore ways to contribute to a more "just and compassionate society".
It added: "Prayer spaces shouldn't be, and aren't being used, to proselytise."
The PSIS statement also claimed the "healing story" mentioned on the 24-7 Prayer International website "reportedly came from a prayer room in a church, and had nothing to do with a school".
A spokesman for the EIS said: "The EIS would have concerns over special interest groups of any type having unrestricted access to children in the school environment … School should never be a place for any external group to promote itself or its policies, views or beliefs."
A spokeswoman for the Scottish Government said: "It is for a headteacher to decide, in full consultation with the local authority and wishes of parents, what links a school should have with its local faith communities.
"Learning about religious beliefs must be delivered within a balanced context."