The Kirk wants the Home Office to overturn its decision not to allow Rev Rola Sleiman, of the National Evangelical Synod of Syria and Lebanon, into the UK on an eight-day visitor visa.
Rev Sleiman, 42, who has a Syrian passport, was reported to be “humiliated by the Home Office response and upset her honesty is doubted”.
As well as speaking at the 2017 General Assembly which starts on Saturday, Rev Sleiman was due to speak at St Giles’ Cathedral.
The Kirk has invited hundreds of overseas visitors to the General Assembly over the years but this is the first visa refusal.
Very Rev John Chalmers, principal clerk to the General Assembly, described the decision as “disturbing and mystifying”.
“We have been looking forward to receiving Rev Rola Sleiman as representative of the National Evangelical (Protestant) Church of Syria and Lebanon at the General Assembly.
“She is the first woman to be ordained in the Middle East and became pastor of her own congregation in Lebanon in February this year.
“Her contribution to our discussion on gender justice and on the situation in the Middle East would be of great significance.
“Therefore we are desperately disappointed at the refusal of the Home Office to issue a visa for Ms Sleiman and we are doing all we can to have this decision reviewed and reversed.
“It is disturbing and mystifying that the UK Visa office has denied her a visa on the basis they do not believe the Church of Scotland is supporting her visit to Scotland, despite calling us and asking for verification, which we gave.
“However, time is not on our side and the fact parliament has been dissolved and MPs are on the campaign trail is making it difficult for us to make headway.
“We remain hopeful more senior UK government figures will overturn this injustice.”
In its decision letter the Home Office stated: “I am not satisfied that you intend to leave the UK at the end of your proposed visit or that you will not live in the UK for extended periods through frequent or successive visits. Furthermore, I am not satisfied that you are genuinely seeking entry for a purpose that is permitted by the visitor routes and that you will not undertake any prohibited activities.”