The crime was only discovered when a guide arrived to open St Michan’s Church for visitors on Monday.
Several other mummies inside the crypt, including the 400-year-old remains of a nun, were left damaged and desecrated after the break in, a spokesperson for The Church of Ireland said.
The Crusader’s body was found turned over inside the crypt.
“I am shocked that someone would target this ancient burial place and desecrate the remains of those lying within it,” the Archbishop of Dublin said in a statement.
“Not only have these individuals desecrated the sacred crypt but they have destroyed these historic mummies which have been preserved in St Michan’s for hundreds of years.”
“I would appeal to those responsible to examine their consciences and return the head of The Crusader to its rightful place.”
David Pierpoint, an archdeacon, described the incident as “devastating and sacrilegious”.
“We are upset at the amount of damage that has been caused,” he said.
“But also the crypt will have to close so tourists will not be able to visit. It is very frustrating.”
Police officers have opened an investigation into the incident.
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