In an open letter to Foreign Secretary Philip Hammond, the church's Moderator Rev David Miller urged the UK government "to do much more to end the genocide and atrocities being reported inside IS controlled regions".
The Surrey-based minister added that following the 2003 invasion of Iraq "we cannot justly wash our hands of the wider security situation" or "deny military help to efforts to overthrow the IS regime of terror".
Reports had highlighted the most barbaric of murders in the IS areas including the beheading of children, he said.
Mr Miller said the Church of England vicar Andrew White, more commonly known as the "bishop of Baghdad", had told the BBC that he and his congregation could be killed for their faith if they continue to gather for worship together.
The open letter has also been endorsed by no less than 52 Free Church ministers across Scotland, as well by its Board of Trustees chairman James Fraser - who was previously principal of the University of the Highlands and Islands.
Rev David Miller, Free Church Moderator said: "We call on the government to join with France, and others, in offering asylum to the clear victims of persecution - irrespective of creed or ethnic background.
He added: "Regardless of the merits of the 2003 invasion of Iraq and its aftermath, we must recognise that our nation contributed to instability in the region.
"This situation has enabled militant Islamist groups, like IS, to thrive.
"We cannot justly wash our hands of the wider security situation, or deny military help to efforts to overthrow the IS regime of terror. He concluded: "We appreciate that this is a fluid situation, and liable to rapid changes on the ground. But the situation of Christians in IS controlled areas is horrific. We cannot stand by and offer only prayer. We urge our government to do more to bring security to the victims of this genocide."