A controversial opt-out clause on gay marriage puts children’s learning and well-being at risk by giving church leaders a greater say than health experts, campaigners warned this week.

The Humanist Society Scotland (HSS) launched a fresh bid on Monday to urge the Scottish government to remove the “radical” clause from its draft sex and relationship education guidance for schools before the official document is finalised.

Campaigners said that the “vague and non-specific conscience clause”, which allows schools and teachers to choose not to cover same-sex marriage, flew in the face of submissions from several health boards. These warned that high rates of teenage pregnancy, sexually transmitted infections and harmful sexual behaviour highlighted the need for comprehensive sex education for all young people, regardless of religious beliefs.

The revised guidelines are being drawn up in response to recent changes, including the passing of a landmark bill legalising gay and lesbian marriages.

However, critics warned that introducing an option to opt out of teaching pupils about same-sex marriage risked fuelling “stigmatisation of LGBT [lesbian, gay, bisexual and transgender] young people, as well as leading to marginalisation of married same-sex couples”.

Gary McLelland, HSS education policy officer, said that the Scottish government should not give religious groups a greater say over pupils’ sex education than health professionals.

“Traditionally it has been accepted that Roman Catholic denominational schools would have special provisions so they could maintain their religious view of marriage, but obviously now that same-sex couples are entitled to marry, it puts them in a difficult position because they don’t want to cover that kind of marriage and that view goes against equality,” he said.

He added that although one in five state pupils attended Catholic schools, falling congregations suggested that fewer and fewer did so for religious reasons.

Launching its campaign against the clause, the HSS pointed out that the previous guidance on sex education - the 2001 Circular - contained no such opt-out option.

It added: “The HSS is concerned that by continuing the current arrangements for religious authorities to provide guidance to denominational schools in Scotland, the educational outcomes and health outcomes for sections of Scottish young people will be diminished.”

A parliamentary inquiry into teenage pregnancy in Scotland highlighted the disparity of provision in sex education and raised specific worries over the lack of teaching in Catholic schools. In Greater Glasgow and Clyde, where one in three schools is Catholic, the health board has also voiced concerns.

The campaign has won support from a number of professionals including the UK philosopher and writer Julian Baggini. He argued that there was a key distinction between personal and civic morality, and that schools were the right places for young people to learn about values and lifestyles they didn’t necessarily share but needed to understand to equip them for life.

He added: “I think people often think that this is about promoting a certain lifestyle, and I would not approve of that, but it isn’t about that. It’s about saying this is what goes on and as a society we think it’s fine.”

Fellow campaign supporter Dr Claire Cassidy, depute head of education at Strathclyde University and a former primary teacher, said: “What I am most concerned about in terms of opting out of sex education, or elements thereof, is that it breaches children’s rights.”

Michael McGrath, director of the Scottish Catholic Education Service, confirmed that the body “supports the rights of all teachers who have conscientious objections to being required by employers to endorse and promote the redefinition of marriage within the new legislation”.

He added: “It cannot be right to force teachers to promote a vision of marriage which is at odds with their own sincerely held views or beliefs.”

A Scottish government spokesperson said that sex education was an integral part of the curriculum, adding: “While individual schools may agree arrangements to accommodate teachers’ personal views, they remain obliged to offer pupils a full, objective and balanced awareness of all aspects of relationships, appropriate to their age.”

The spokesperson said that guidance on this subject was currently being considered and was expected to be shared with schools by the end of the year.