Non-denominational schools are at risk of being turned into de facto state Protestant faith schools, according to claims from secular campaigners after a year-long investigation.
Concerns have been raised that the role of chaplaincy is extending into more aspects of school life, allowing religious groups to "proselytise" to children.
Edinburgh Secular Society (ESS), which conducted the countrywide research with help from the National Secular Society, said that large chaplaincy teams - rather than individual chaplains - are becoming more common in schools, and claimed that these teams include members with "more fundamentalist views", such as creationism and faith healing.
The group, which scrutinised religious groups' websites and other publicly available information, said that chaplaincy teams regularly had six to eight members in both primary and secondary schools. One secondary - Larbert High, in Falkirk - has 10 members on its chaplaincy team, the ESS found.
Jon Reid, headteacher at Larbert, said that the size of the chaplaincy team reflected the local community and the faiths within it; the team includes representatives from the Church of Scotland but also Larbert Pentecostal Church, Larbert Baptist Church and the Free Church of Scotland.
There is "no hidden agenda whatsoever", he said, and no compulsion on students to attend the once-a-term services. The chaplains help with events from Holocaust Memorial Day to school barbecues, Mr Reid added. "We are very proud of the role of the chaplaincy team. It is appropriate, measured and proportionate, and long may it continue."
But the ESS said that most people perceived the role of chaplain as that of a single minister performing a statutory minimum number of religious assemblies. In the past five years there had been a deliberate policy to expand the role of chaplain to "a far more pervasive, indeed claustrophobic, involvement in school life", it said.
A recent document from the Church of Scotland, highlighted by the ESS, says that chaplains may take part in activities including "accompanying pupils on an excursion, sharing a meal from time to time with staff and pupils and participating in parent council activities".
"This expansion of the chaplaincy role being promoted by the Church of Scotland, and of other initiatives. has the potential to see non- denominational schools effectively turned into state protestant faith schools," says the ESS report, seen exclusively by TESS.
There is "compelling evidence that evangelical and proselytising Christian organisations are targeting and accessing non-denominational schools", the report states, adding that this results from "a well-organised and deliberate policy orchestrated, in the main, by the Church of Scotland in partnership with the Scripture Union".
ESS founding member Norman Bonney said that Scottish government guidance on religious observance in schools provided shelter for "evangelising bodies to step into our schools to influence the education of our children".
But the Rev Sandy Fraser, convener of the Church of Scotland's education committee, hit back at the criticism. "The Church of Scotland is increasingly disappointed in the nature of these comments by the Edinburgh Secular Society," he said.
"It is extremely inaccurate to suggest chaplains inveigle their way into schools. Chaplains and other community figures are in schools by invitation of the headteacher to assist in whatever way the headteacher feels is helpful to the school. Chaplains are very clear that their job is not to impose their views on the school community."
A Scripture Union Scotland spokeswoman said that her organisation agreed with ESS that "pupils have a right to hear about different faith perspectives, and that proselytising within a school context is wholly inappropriate".
She stressed that Scripture Union Scotland work took place at the invitation of schools, across all denominations, and was supported by Scottish government guidance.
A Scottish government spokeswoman said that it was "for a headteacher to decide, in conjunction with the local authority and wishes of parents, what links a school should have with its local faith communities".