A group that promotes church security says attacks on mosques and temples are taken more seriously than those which target churches and vicars.
An Anglican priest suffered black eyes, cuts and bruises in an attack
Nick Tolson, of Churchwatch, told BBC Radio 4 that the community feels police put more resources into investigating religious attacks on non-Christians.
Mr Tolson said assumptions of a hate-crime are made when Muslim and Jewish religious sites are attacked.
His comments come after a recent attack on an Anglican priest in east London.
Mr Tolson said: "What we tend to find is that, if a mosque or a temple is attacked, quite often it is looked at as being a faith crime until proven otherwise.
"With churches it's taken as being a normal crime unless it can be proved to be a faith crime."
But Peter Fahey, from the Association of Chief Police Officers on race and diversity issues, dismissed Mr Tolson's suggestion saying attacks on mosques or temples were easier to identify as faith-hate crimes.
"Sometimes it is easier to identify that an attack on a mosque or a temple is a faith hate crime when sadly churches are already suffering vandalism or theft because of some of the treasures they have within them, and that can be more difficult."
Muslim community leaders in Tower Hamlets, east London, condemned the 5 March attack on Canon Michael Ainsworth, 57, which police did categorise as a "faith-hate" crime.
Canon Ainsworth was attacked by two youths while a third watched him being beaten in the churchyard of St George-in-the-East.
The attackers jeered at the priest, who suffered cuts, bruises and black eyes, for being a churchman.
However, Mr Tolson said he was not convinced the attack on the canon was a faith-hate crime.
"Although there were some detrimental terms used by the attackers about him being a priest I think that the main issue was that no-one should try and move on a group of youths on their own as this puts them at risk," he said.
"I am aware however, that the congregation feel intimidated... this is true for any gathering of youths in a churchyard, regardless of the youths' religion, they are intimidating," he added.