One of the most controversial issues in Scottish education has been the influence of religion in schools.

The debate thus far has tended to focus on the separate system of state-funded Catholic schools, which critics argue creates division, harbours sectarianism and should therefore be scrapped. The church has been equally robust in defending its position, insisting the attacks are bigoted and that faith schools are a manifestation of the freedom and democratic principles of Scotland.

Such polarised exchanges, usually couched in hyperbole, have always attracted media attention and usually excite a flurry of activity on the letters pages of national newspapers, although none has made the slightest difference to the status quo thus far. All that might be about to change.

In recent times, a very different approach has been taken in opposition to religious influence in schools which owes more to the new atheism of writers such as Richard Dawkins and Christopher Hitchens than it does to traditional tribalisms.

The latest attacks from secular and humanist groups seek to challenge specific issues of educational policy or educational legislation rather than simply decrying the influence of religion per se. Crucially, they also widen the debate to target religion in non-denominational schools.

Last year, the Humanist Society Scotland began this approach by arguing the legal right of parents to withdraw their children from religious education and religious observance was being widely ignored across all state schools. Earlier this year, the Glasgow-based organisation Secular Scotland raised a petition at the Scottish Parliament calling for a change in the law to make it easier for parents to opt out of religious observance.

The most recent intervention came last week from the Edinburgh Secular Society,which called for new legislation to overturn the legal right of religious representatives to sit on council education committees. Under the 1994 Local Government (Scotland) Act, councils have to appoint at least three members from churches, with at least one from the Catholic Church and another from the Church of Scotland.

Anyone who doubts the effectiveness of such an approach need only look at a recent National Secular Society complaint to the Office of the Scottish Charity Regulator about the Glasgow-based St Margaret's Catholic adoption agency, which led the body to conclude that it had broken both equality and charity law by excluding same-sex couples – effectively shutting it down.

The church hierarchies are now acutely aware they are facing a new challenge and Archbishop Gerhard Müller, one of the Vatican's most senior clerics, used a visit to Scotland only last month to reinforce the message that the provision of faith schools by the state is a fundamental right of Catholic families.

While the current battles in education have not thus far attracted the headlines afforded to outspoken attacks on Catholic schools or the vociferous rebuttals of the past, they may have far greater impact and require a response from the churches that is as much rooted in legal advice and political influence than it is in doctrine.