Scottish independence: Free Presbyterian Church of Scotland warning
The Free Presbyterian Church of Scotland has claimed independence would weaken the position of the Christian church "at the heart of the nation".
It said the Treaty of Union secured the Protestant religion and Presbyterian church and any change "would be a provocation of God".
Education Minister Alasdair Allan said the SNP had no plans to alter the present role of the established church.
The Western Isles SNP MSP said it was respectful of the role of religion.
Free Presbyterian Church of Scotland spokesman, the Rev Allan MacColl, told BBC Alba that religion and morality were in a "terrible" state across Britain.
He said: "But present constitutional arrangements guarantee Christian religion in its position at the heart of the nation, and defends the position of the church and the Bible clearly teaches that.
"It is the duty of all nations to recognise the position of Christ church and any move away from that would not only be dangerous for the church, it is dangerous for the people."
The Rev MacColl added: "We are very uneasy about any move to secularize, or even change the existing arrangements."
He said the church could not tell people how to vote in a referendum on independence, but could warn them.
Mr Allan said the Synod of Free Presbyterian Church of Scotland had expressed similar views in the past.
He said: "To refer to some of the issues raised by the Synod, however, it should be stressed that the SNP has no plans to alter the present role of the established church upon independence, and is respectful of the role of religion in Scotland.
"The SNP would also keep the Queen as head of state after independence."