The Kirk responded after claims it would be legally powerless to stop any minister conducting gay marriage ceremonies when the law in Scotland is changed.
A spokesman said no matter what legislation the Scottish Government proposed, ministers were bound by Church law.
However, the Reverend Lindsay Biddle, chaplain for the liberal group Affirmation Scotland, claimed she expected a dozen congregations who had signed up to the group would conduct gay marriages in their places of worship.
Ms Biddle, whose husband is minister at St James Parish Church in Pollok, Glasgow, insisted the decision to marry any couple rests with the minister.
She said: "I would not conduct the marriage of a heterosexual couple, for example, if I thought one of them was being abused, if I thought age was a factor – if a 50-year-old was getting married to a 16-year-old – or if I thought they had significant differences they have not worked through.
"There are other ministers who will not marry a couple who have had pre-marital sex or if they have had children.
"Nobody, either in the Church or the local authority, forces me to do a marriage or challenges me why I do or don't do a marriage. The same will apply to people of the same gender.
"A church or authority will not be able to question the decision of the minister to join or not to join a particular couple. It is not like I can sue the Catholic Church for not marrying a Protestant to a Catholic."
Last night a Kirk spokesman hit back, saying: "These are hypothetical questions, but the Reverend Lindsay Biddle is quite wrong in her claims.
"Under the law of the Church as it currently stands, a minister can only solemnise a marriage between a husband and wife (Act 1, 1977).
"No matter what legislation the Scottish Government proposes, all ministers will be bound by this Act until, or unless, it is changed by the General Assembly.
"If the General Assembly decides the Church of Scotland should, as a denomination, opt out of conducting same-sex marriages, then any minister who conducts a same-sex marriage would be subject to Church discipline.
"Until we have seen the details of the proposed bill we will not comment on the hypothetical demands it might make on the General Assembly or on individual ministers."
The Herald understands the prospect of ministers carrying out same-sex marriages would be the tipping-point for some clergy already considering quitting over the issue of gay ordination.
Previously one in five Church leaders said they would leave if gay ordination was allowed, and if their flocks followed them it could mean 100,000 quitting the Kirk.
Facing its greatest schism in centuries after openly gay Scott Rennie was appointed a minister in Aberdeen, the Kirk's stance on homosexual ministers will be tested finally at next year's General Assembly.
Same-sex marriage will also now be under consideration at the crunch annual gathering.
One evangelical source said those opposed to gay ordination have the same standpoint on same-sex marriage.
He said: "The issue of ministers conducting gay marriages will have the same effect on Church members as gay ordination. It will be raised at the same time as gay ordination and I would expect the Church would have to make a decision on that [same-sex marriage] next year."
A ballot last year showed 19.4% of Kirk Session members – the first court of the Kirk made up of ministers, elders, deacons and key parishioners – said they "would consider it obligatory to leave the Church" if people in same-sex relationships are allowed to marry.
The Rev Ian Watson, of Kirkmuirhill in Lanarkshire, said allowing gay marriage would have a detrimental effect on society. He said: "The Scottish Government can call it marriage, but it is not marriage."
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