Speaking after First Minister Nicola Sturgeon announced her plans for another referendum on the issue - two and a half years after a previous vote - the Convenor of the Church and Society Council at the Church of Scotland also said it will stay neutral.
Rev Dr Richard Frazer said: "...the First Minister has declared her intention to seek the authority for a referendum on Scottish Independence.
"And with a majority of MSPs in favour of independence it is likely that such a vote will be passed. The UK Parliament will have the final say on whether to grant the right to hold an Independence Referendum.
"It would be wrong if it was withheld."
Taking a neutral position during the 2014 Scottish Independence Referendum, the Church says its stance will remain the same during any future vote.
Dr Richard went on to say: "In 2014, rather than taking a position on either side of the independence debate, the Church of Scotland consulted individuals and communities on what sort of Scotland they wanted to live in.
"It also hosted, and encouraged others to host, respectful conversations where people expressed their position passionately but with courtesy and a strong commitment to listen.
"Individual church members will always be entitled to their own views but the Church retains a position of active neutrality on the matter of Scottish Independence."
He also warned against people allowing debate around the issue of Scottish independence to become "divisive and acrimonious".