Full planning permission has been granted to convert a derelict building in the town centre.
The Outer Hebrides Presbytery of the Free Church of Scotland Continuing said it is a “most unwelcome development.”
The denomination says its main concern is with the religion of Islam itself.
The FCC stresses it has “nothing against individual Muslims, least of all any who have been forced to flee their homelands because of persecution and suffering.”
In a statement the presbytery said: “If a mosque ever opens, Islam will be able to promote itself in our midst through public worship, despite its beliefs and practices being alien to the religious convictions of the vast majority of our community.”
It added: “We urge the Lord’s people to make this situation a matter of earnest prayer, asking the Almighty that in His kindness He will grant that no mosque will ever appear in Stornoway.”
The church said Islam is “wholly inconsistent” with the Biblical teachings and is “opposed to the Christian religion.”
The statement added: “Islam is also incompatible with, and indeed a threat to, our religious and civil liberties.”
The Free Church of Scotland Continuing (FCC) has criticised a proposal to build a mosque in Stornoway.
Church hits out at Stornoway mosque plans
11 Sept 2017