Six congregations have quit, half in the Kirk's financial heartlands. There could be a bigger impact on Kirk coffers as ten more quit in the next two years.
In Edinburgh, Holyrood Abbey Church worshippers give £215,000 a year, New Restalrig gives £114,000 and St Catherine's Argyle collects £196,000. Gilcomston South in Aberdeen brings in £300,000. On Lewis the Kinloch and Stornoway churches together bring in £210,000. In total, the Kirk got £60.5m in givings in 2011.
The developments came as father-and-son ministers said they would quit the Church over the move to let congregations ordain gay ministers made at its May General Assembly. The decision still has to be ratified.
The Rev David Randall of Ayrshire has followed his father the Rev David Randall senior of Logie St John's in Dundee as the latest to anounce he will leave.
The Ayrshire minister said: "I have always just felt it seems they are willing to pursue this liberalising pro-gay agenda regardless of the cost and it is emerging the cost is going to be very high."
About 10 congregations are understood to be in negotiations with the Kirk to leave over gay ordination.
A Church of Scotland spokeswoman said: "The loss of any minister or member would be very disappointing given it is so early in the process of decision making on this matter, with a final decision not due until 2014 at the earliest." She added: "We do not anticipate a serious effect on the budget and our overall finances."
Rebel Kirk congregations are being wooed by the Free Church. The traditionalist Free Church is understood to have set up a working group to talks to congregations that are unhappy with the decision on gay ordination.