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.
"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".