In June this year, the society raised a petition together with Inverclyde parent Mark Gordon to change the system from opt-out to opt-in.
They argue that although parents who do not wish their children to be involved in religious observance are allowed to withdraw them, the children are not offered a suitable alternative activity.
"Our petition seeks to change the Education (Scotland) Act 1980 so that children are not automatically opted into religious observance by the school," the society said.
"It asks instead that parents are given an active choice between religious observance and a suitably meaningful alternative activity. In essence, we want the parents to be asked first."
The group is presenting its case to the Public Petitions Committee, which is meeting today to discuss the issue for the first time.
The Scottish Secular Society will argue that a change in demographic and religiosity in Scotland justifies the move, and that the Scottish Education Act of 1980 conflicts with human rights legislation and a 2007 European Court ruling stating that the right to opt out must be practical and not illusory.
The society will present testimonies from parents whose children, after being withdrawn from religious observance, were left unattended in corridors or told to carry out menial tasks like sharpening pencils or cleaning the library.
"The petitioners consider the right to opt out of religious observance to be illusory and impractical and since the law facilitates this it must be changed," said a spokesperson for the campaign.
The Free Church of Scotland has challenged the recommendation, arguing that the majority of Scottish parents are happy for their children to take part in religious observance.
The Reverend David Robertson, a Free Church minister in Dundee and director of the Solas Centre for Public Christianity said: "Statistics go against the Scottish Secular Society - they are a tiny group of people who are seeking to impose their will and their philosophy on the vast majority of Scottish parents."
He added: "It is clear that the secular society wish to eradicate any form of religion in any public school. Solas CPC, the Free Church, and many other Christian churches and organisations will resist this secular tyranny as much as we possibly can."