The Church of Scotland and the Humanist Society Scotland are preparing a joint plan to put to MSPs to replace religious assemblies in schools with a "Time for Reflection" slot.
The petition to MSPs will suggest that pupils opt in to religious observance in schools instead of being able to opt out as at present.
The Rev David Robertson, Free Church of Scotland minister in Dundee and director of the Solas Centre for Public Christianity, said: "We have the extraordinary situation where the Church of Scotland, which claims to be the Church of John Knox, is undermining his core policy, that there should be a Christian school in every parish."
He added: "If the Church of Scotland stab-in-the-back for Christianity is accepted I would suggest Christians should automatically opt their children out of this compulsory State godless religion.
"It would be far better to have meaningful Christian worship which pupils and teachers could opt in to, rather than force everyone to go to the beige, bland, brain-dead, unquestioning banalities that would … result."
The Church of Scotland and the Humanist Society of Scotland say legislation to change the name of "Religious Observance" to "Time for Reflection" would make such periods more inclusive after concerns over gatherings where one belief system is said to have been promoted over another.
The Rev Sally Foster Fulton, convenor of the Church of Scotland's Church and Society Council, said earlier: "Regular, inclusive Time for Reflection will enhance young people's ability to celebrate difference."