Congregations have begun to resign from the Church of Scotland, with six having already quit, over a recent decision to allow gay ministers to be ordained.

Despite the decision still having to be ratified, it has been estimated that the church could lose £1 million a year in givings, as congregations quit, having a potentially strong impact on the coffers of the Kirk over the next two years.

Traditionalist congregations are believed to be offering financial support to congregations with less money, if they wish to also leave the church.

The Kirk brought in £60.5 million in givings in 2011.

Edinburgh congregations having left, or voiced intention to leave include Holyrood Abbey Church, at £215,000 a year, New Restalrig at £114,000, and St Catherine’s Argyle at £196,000. In South Aberdeen, Gilcomston brings in £300,000 a year, and Lewis the Kinlock and Stornoway bring in £210,000 combined.

The decision to allow gay ministers to be ordained was made at the May General Assembly, but has not yet been ratified. Reverend David Randall of Ayrshire, and his father Reverend David Randall Senior of Logie St John’s in Dundee, both said they would leave.

Reverend Randall Snr 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. That is inevitable. There have been warning voices over the last three or four years that have just been ignored. It’s very sad.

“It’s interesting that the church is making statements about not being in crisis … the fact they make those statements is quite revealing.”

The Herald Scotland reports that ten congregations are in negotiations with the Kirk over the issue of whether to leave.

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.

“The Church of Scotland has an annual budget of around £120m. It is far too early to predict the precise effect of a drop in givings from the very small number of ministers and members who have given early indications of a wish to depart. We do not anticipate a serious effect on the budget and our overall finances.”

The Free Church is reported to be in negotiations with defecting Church of Scotland congregations, and has set up a working group to hold talks with those unhappy because of the change.

Congregations began threatening to leave after the announcement was made in May.