Canon Andrew White is currently in Jerusalem after leaving Baghdad last week and said in a Facebook post he had been warned that returning to the city would be too dangerous.
Islamic State (IS) fighters are thought to be just a few kilometres away from the capital and Iraqi troops are struggling to hold them back.
Canon White is known as the Vicar of Baghdad because he was the only Anglican priest there.
He has now revealed he will return to Iraq, but not to Baghdad.
On Facebook, he said: "I have just had a wonderful conversation with my dear friend the Archbishop of Canterbury.
"He has agreed for me to return to Iraq, though not to be based at the Church in Baghdad.
"It was such a good conversation and we ended it by saying how much we loved each other. I do indeed love my Archbishop Justin. Blessings from Jerusalem."
Canon White had already hinted on Premier's News Hour that he would like to return to another area of Iraq regardless of the risk from IS militants.