Archbishop of York David Hope has said violent assaults on clergy and burglaries from churches are making some vicars too frightened to take up posts in inner city areas.
The archbishop installed security doors at his home
The archbishop told BBC Radio 4's Today programme the stress and trauma caused has made it "extraordinarily difficult" to attract clergy with families to the positions.
His comments come after the recent publication of research which shows that vicars now stand more chance of being threatened or assaulted than police officers.
Dr Hope - the second most powerful cleric in the Church of England - said many clergy enter the profession with brave intentions but have little idea of what may lie in store for them.
By the time they are ordained numerous stories of vicious attacks on vicars and even nuns
persuade many to seek less dangerous dioceses.
The effect of this rush for safer parishes leaves some of the worst affected areas with few, if any, applicants.
"There is a distinct lack of applications and we are finding it very difficult to fill posts, particularly in the north and in some of the more difficult urban areas," he said.
"To some extent I understand that if a person is married with a young family.
"Who would want deliberately to take their family into these situations?"
The archbishop recently appointed a former deputy chief constable to take charge of security in his diocese and installed security doors at his own offices at Bishopthorpe Palace near York.
He said one church in his diocese has been burgled 28 times in two years
Some clergy have become so frightened they have removed vicarage signs to stop their homes being targeted.
But Dr Hope maintained every effort will be made to reassure worried clergy by continuing to issue panic alarms, CCTV cameras and specialist advice on personal security.
The Reverend Paul Andrew, of St John's Church in Hammersmith, has taken up the offer of self-defence classes from the union Amicus.
He said thieves had stripped almost everything of value from his church.
But he said other parishes had been less fortunate.
"In one of the parishes half a mile away the parish priest was murdered in his vicarage and a local Roman Catholic priest had petrol poured through his letterbox and his presbytery set on fire," he said.
"Another was actually shot with a shot gun."
The self defence classes, as well as additional security to his home, have helped Mr Andrew feel safer.
"One needs to be able to feel you can walk the streets with some confidence, not worrying about every shadow that passes you," he said.