Revd David Robertson compared the birth of Jesus with life in present-day Scotland, and said that atheists hiding under the guise of "secularism" were attempting to "remove all traces of Christianity from society".
The leading churchman, who takes up the role of Moderator in May, said it was pointless in Christians having faith if it did not affect their motivation in the workplace and the community.
In his Christmas message he said: "At every nativity one of the facts that is put across is that 'there was no room at the inn' for baby Jesus. It strikes me as a suitable metaphor for how much of Scotland will celebrate his birth this year.
"Some will have no room for Jesus because they are too busy watching TV, feeding themselves or getting whatever presents they can.
"The glitz, consumerism and greed leave little place for Jesus. And yet still people struggle to find satisfaction.
"Others want to exclude Christ from Christmas in order to be 'inclusive'. But 'Winterville' or 'seasons greetings' is not the real problem.
"No the real problem are the atheists and agnostics who, under the guise of 'secularism', want to remove all trace of Christianity from society."
His comments come less than a fortnight after the Free Church accused some secularists of a sectarian attack against Jim Murphy.
It said comments about the new leader of the Scottish Labour Party's faith were unacceptable.
Revd Robertson added: "They want to remove religion from public life.
"This essentially means they want to remove Christians from public life, as we have recently seen with Jim Murphy MP, because no Christian is going to hold to an internalised faith only, which doesn't affect their outlook in every part of their lives.
"The secularists will continue these witch hunts until Christ is removed from public life and we end up with a Godless dictatorship.
"For them, there is no room for Christ in the inn of the brave new world of modern Scotland."