Church leaders say they did not know one of their hospital chaplains wanted a sex change.
Officials of the Diocese of Chichester said they were unaware the priest, who has worked in a Sussex hospital for less than a year, had undergone months of hormone therapy and intended to have surgery.
Yesterday they said their first concern was for the welfare of the priest who had left home and threatened to quit after his plans became public.
The Reverend David Guest, diocese spokesman, said: "We did not leak this information because the church did not even know about it.
"We are not tearing our hair out, saying it is disgraceful. Instead our prime aim is to care for him and give support. We are not concerned about anything else at the moment."
A friend of the hospital chaplain said he was "frightened" and had left his home since the news was leaked to the Press.
She said: "He is frightened and will do anything not to be identified. He has already spoken about giving up his job, transition and much worse.
"He is a sensitive person who wants to keep his life private."
His future in the Church of England lies in the hands of the Bishop of Horsham, the Right Reverend Lindsay Urwin, who will decide if the priest's licence will be revoked.
He is taking charge because John Hinde, the incoming Bishop of Chichester does not take up his position until May.
Mr Guest said: "The Bishop of Horsham is now taking time to consult and pray on the matter. We have made sure the man involved has got someone to speak to and a good degree of counselling."
Only two people at work had known he was transsexual. A hospital spokeswoman said: "This is a personal matter between ourselves and a member of our staff."
If the church decides to revoke the priest's licence, it will be down to the hospital which employs him to decide his future.
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