The Syrian Reverend Rola Sleiman, 42, was denied a visa by the Home Office, despite the Church backing her visit, the BBC reported.
In a statement on Tuesday, the Home Office said it did not comment on individual cases but each application was considered on its merits and evidence provided.
Sleiman is a representative of the National Evangelical (Protestant) Church of Syria and Lebanon.
She took up a new post as parish minister in Lebanon in February.
But Sleiman received a letter from the Home Office on May 8 saying that it was not satisfied that her income was what she claimed and that the Church was going to support her financially, reports the BBC.
The letter read: "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 you will not undertake any prohibited activities."
Church leaders have branded the decision "disturbing and mystifying".