The Scottish Secular Society has lodged a petition calling for the default position by councils to be that children do not take part in these events and must "opt in" if they wish to do so.
A spokesman for the Scottish Government's Curriculum Unit said there was no evidence to back up the Secular Society's stance.
He said: "The Scottish Government believes that the current legislation and guidance around religious observance is relevant and up to date and is not persuaded based on the evidence given that a move to an opt-in system would be helpful to young learners."
The document said "it can offer opportunities for young people to reflect meaningfully on different points of view and values, including their own". It said: "It creates chances to think about the nature and possible meaning of life and humans' place in the world."
"It can promote critical thinking, supporting the development of awareness that not all people think the same or share the same ideas and experiences about life."
The Church of Scotland said it welcomed the Government's stance while Reverend Sandy Fraser, Convener of the Kirk Education Committee, said there were misconceptions about the modern form of religious observance.
He said: "Chaplains are only ever there if the school invites them in. They are not trying to convert children. They are essentially raising awareness of spirituality, of otherness, a sense of something other than materialism."
A Scottish Secular Society spokesman said: "The Church of Scotland shows its customary confusion.
"We at the Scottish Secular Society, who authored this petition, support religious observance if it's inclusive, non-confessional and truly non-denominational. Sadly, as we found out from the steady stream of complaints from parents, a stream which continues even as we speak, this is not the case in many Scottish schools."