Representatives of Secular Scotland said it was routine for the only alternative to assemblies to be for pupils to sit in the school office or in a corridor.
It was also suggested pupils were given Creationist material to take home, despite their parents desire for them not to be included in lessons about religion.
The claims were made as the society gave evidence to MSPs on the Scottish Parliament's public petitions committee.
The committee is considering a petition from Secular Scotland and Inverclyde parent Mark Gordon which calls for a change in the law so parents are asked before their children take part in religious activities rather than having to opt out.
Scottish novelist Christopher Brookmyre, Andrew Copson, chief executive of the British Humanist Association, and the Richard Dawkins Foundation for Reason and Science have backed the petition. Mr Gordon said research suggested only 20% of parents said their school had informed them of their opt-out rights.
However, Jackson Carlaw, a Scottish Conservative MSP for the West of Scotland, said it could benefit pupils to take part in such events while being encouraged to make up their own minds about what they believed in.
The Church of Scotland said schools' religious observance is "focused on the beliefs and values that shape and are shaped by each school community".