The move is a new cash blow with the two congregations contributing £315,000 between them to the Church.
One of the congregations has already left, with the second negotiating terms.
The departure of St Catherine's Argyle, in the leafy Grange district of Edinburgh, and New Restalrig in Willowbrae, also in the Scottish capital, comes as almost 1000 key figures are due to gather for the annual meeting of the Church in the city in May.
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The two confirmed breakaway congregations are in the "higher givings bracket" and so among the wealthiest in terms of donations.
Reverend Robin Sydserff, minister at St Catherine's Argyle, is understood to have strong support in his congregation - which generated income of £200,000 a year - in objecting to the direction of the debate over the issue sparked by the appointment of openly gay Reverend Scott Rennie to an Aberdeen church in 2009.
A move was made to allow the ordination of gay ministers at the General Assembly last year, sparking a number of resignations by congregations. Reverend David Court, formerly of New Restalrig, whose congregation donated £115,000 a year, has also now officially signed off, or demitted, from the Kirk and has become a member of the Free Church of Scotland.
His flock of more than 100 now worship in a mission hall in Craigentinny in the city, with New Restalrig under the guidance of locum minister Reverend Peter Nelson.
Although Mr Sydserff is said to have support, one Kirk source said the flow of worshippers can vary in urban presbyteries, adding that St Catherine's Argyle had "long been a magnet" for evangelicals.
A locum minister will also be appointed for the Grange church and the St Catherine's Argyle parishioners who stay with the Kirk.
Parish census records showed 700 Kirk-affiliated worshippers at St Catherine's Argyle, while more than 2000 were Kirk-affiliated in New Restalrig.
Around 12 out of 1400 congregations are understood to be involved in negotiations to quit the Kirk, and givings, which in total were worth £60.5 million to the Church in 2011, will also be a consideration in each case.
Ministers who have left or indicated they will leave include those in parishes such as Holyrood Abbey Church which gives £215,000 a year, St George's Tron in Glasgow that raises £300,000 and Larbert Old Church, Falkirk that feeds £110,000 a year through Kirk coffers. Mr Sydserff declined to say where parishoners would worship following the split. It is understood the use of the church hall is negotiable.
He said: "Both our internal consultation over the past year and the Presbytery's formal consultation have indicated that our decision has the backing of the vast majority of the active congregation.
"Discussions with the Presbytery of Edinburgh as to the practicalities of separation have been ongoing for a number of months.
"These discussions have been positive throughout."
Mr Court, now leading his flock under the title of Christ Church Edinburgh, said: "There is of course a real materialistic challenge leaving the Church of Scotland with the stipend and the manse, but I don't regret my decision for a moment."
He added: "I am free to proclaim the Gospel of Jesus Christ, and it is a wonderful experience to be supported both by my congregation and my colleagues in the Free Church"
The Church declined to comment last night.