It comes as the leaders of the three strands of Christianity which have worshipped at the site of Bothwell Parish Church over the course of more than 1400 years unite to save the building.
A Catholic church, St Brides, since the sixth century until the Reformation, the church served a relatively short spell as an Episcopalian place of worship before becoming Bothwell Parish Church in the early-1600s.
The original foundations of Scotland's oldest collegiate church bore deep under today's structure but the building has been rebuilt over time, particularly after the tower crashed through the roof - twice.
Now the heavy stone roof slabs over the medieval quire, built by Archibald "The Grim" the Third Earl of Douglas in 1389, are causing the supporting walls to bulge and the church has a year to save this section of the building, with £2 million needed for the work.
The Prince of Wales has given a substantial donation to the fund, said Reverend Jim Gibson, the parish minister who also serves as chaplain to the Queen in Scotland.
He added: "This is a very special church and what we want to do is save this building given its historic and architectural value and the engineers and the architects want this done as quickly as possible."
It is thought to be the second time that he has given money to the church. In the 1970s he apparently made a donation to a similar restoration fund.
The fundraising campaign is being supported by Archbishop Tartaglia, of the Diocese of Glasgow; The Rt Rev Dr Gregor Duncan, the Episcopalian bishop of Glasgow and Galloway and The Very Revd Professor Iain Richard Torrance, Dean of the Chapel Royal.
Archbishop Tartaglia said: "I am delighted to support the efforts being made to preserve Bothwell Parish Church which has a long and distinguished tradition dating back long before the reformation. Indeed it was the Pope who granted it special status back in the 14th century as a collegiate church.
"Though the upheavals of the reformation brought profound distress and pain, ours is a more ecumenical age and so I am comforted to see a building which has had such a fascina- ting and colourful history continue to serve as a place of Christian worship on a site which has been hallowed since the sixth century."
The church has so far raised £1.3m for the restoration project, with £700,000 raised by the congregation.
Prince Charles, who would become head of the Church of England when he ascends the throne, has hinted that as king he would take the title of "Defender of Faith" rather than "Defender of the Faith", which is used by the Queen and was bestowed on Henry VIII by the Pope in 1521 for his early support for Roman Catholicism.
A Clarence House spokesman said: "The Prince of Wales has given his support to a number of church restoration projects across the country."
In 2011 he became a patron of a Norfolk church's fundraising appeal when he also made an undisclosed donation to the project at St Peter and Paul's Church in Walpole St Peter.
In 2004 he also made a "generous" donation to a £500,000 appeal to save the Strawberry Hill Gothic Church in Shobdon, near Leominster, Herefordshire, from deteriorating.
Through his Prince's Charities Foundation, he famously ploughed £20m into Dumfries House to save the stately home for the nation. The funding meant that the mansion house, completed by the Scots-born Adam brothers in 1759, and its original collection of Chippendale furniture, was saved and opened to the public.