Rev Jan Steyn and wife Linda, originally from South Africa, have been denied citizenship on the basis that he is working, temporarily, in Paris, where he is serving the Scots Kirk.
The couple are well known in the area – Rev Steyn was the minister of St John’s and Dairsie United Parish Church for five years.
Mr Steyn (57) described the applications being denied as “devastating”.
He said: “Having our applications for citizenship denied by UK Visas and Immigration was devastating news.
“I work for the Church of Scotland, a UK-based organisation, and we plan to return to the UK which is our base and the family home that we own is in Cupar.
“This decision has thrown our lives and my ministry into indescribable uncertainty and turmoil.
“I realise citizenship is not our right and is actually a privilege.
He added: “There are guidelines for the process but someone, somewhere decided to ignore the UKVI’s own guidelines without reading the provided documents properly, speaking to us or the organisation that I work for.
“Someone made a judgement on our intentions based on a misinterpretation of a letter which actually confirmed our commitment to serving through a UK-based organisation.”
MP Stephen Gethins raised his case at PMQs, asking Theresa May to look into the “grave error”.
He said: “The Home Office must look at the correspondence properly.
“They have ignored the fact the South-African born couple moved here a long time ago, bought a permanent home here and that Mr Steyn is an employee of the Church of Scotland where he will continue to work when his time in Paris comes to an end.
“Although the couple have Leave to Remain in the UK, the decision to deny them citizenship has been very stressful and it is clear the Home Office has once again failed to look at the facts.
“Rev Steyn and his wife have made a huge contribution to the Cupar area and will do so again.
“The Home Office has denied having immigration targets to meet but grave errors have been made in this case and they need to own up to it.
“They deserve much better.”
The PM has assured Mr Gethins that the Home Secretary will “look carefully at the case”.
Mr Steyn followed in the footsteps of a legendary Second World War hero Rev Dr Donald Caskie, who was known as the Tartan Pimpernel, when he took up his post in Paris.
A Church of Scotland spokesman said: “Mr Steyn is a valued minister of the Church of Scotland, whether he is in our congregation in Paris or one of our charges in Scotland. We value his ministry and want him to continue serving with us in the future, whether it be in the Church of Scotland congregation in Paris, or Scotland in the longer term.”