It follows a decision by the Public Petitions Committee took evidence from the Scottish Secular Society on Tuesday 11 November, and decided to write to the Scottish Government and educational bodies for their views on the matter.
Ken Cunningham, general secretary of School Leaders Scotland, also accused the Scottish Secular Society of using "inflammatory rhetoric" after two representatives urged MSPs to outlaw teaching that God created the world, and instead only present the evolutionary account of human origin.
The intervention from School Leaders Scotland has been welcomed by Revd David Robertson, the next Moderator of the Free Church of Scotland.
Previously Mr Robertson said the Scottish Secular Society were "raising the false bogeyman of creationism" in their effort to banish all traces of Christianity from Scotland's schools.
The Scottish church leader commented: "It is interesting that School Leaders Scotland has spoken about the secularists' use of 'inflammatory rhetoric' in their petition.
"This demonstrates that the Scottish Secular Society are simply trying to scaremonger, and we hope that our MSPs have the sense, intelligence and backbone not to give in.
"The body of secondary school teachers are stating what the current situation is, whereas the Scottish Secular Society were able to offer no evidence whatsoever that creationism was being taught in science classes in Scotland's schools, and we politely ask our atheist friends to stop wasting parliamentary time with their sensationalised nonsense."
Mr Robertson continued: "I may be kind of old-fashioned but my view is that science should be taught in science classes - not religious or anti-religious philosophy.
"If atheists choose to believe that the universe created itself out of nothing that's up to them - but please don't seek to impose your faith upon the rest of us.
"Can we not encourage children to think about the issues for themselves, rather than just tell them what to believe?"