Dr Keith Laidler says the head is at the 15th century Rosslyn chapel in Midlothian.
He became interested in the possibility after reading a book which claimed the Knights Templar had a head which they worshipped.
One theory is the head was carried to Scotland by Mary Magdalene via France.
But another has it that the Knights Templar, a religious military order born out of the first crusade, dug it up in Jerusalem and carried it through France to Scotland.
Dr Laidler, who lays out his ideas in his book The Head of God - the Lost Treasure of the Templars says there was a cult of heads in the Middle Ages.
Scottish Catholics - no faith in head theory
But Father Danny McLoughlin, a spokesman for the Roman Catholic Church in Scotland, branded the idea outrageous and impossible to believe.
''The Templars disappeared in Scotland in the 13th century and that chapel was not built until 300 years later so there seems to be a slight problem there to say nothing of the other problems we would see,'' he said.
''The head that the doctor is talking about has yet to appear and perhaps what I should say is bring me that head and let's run some tests on it, and if you can prove that head sat on the shoulders of Jesus Christ then maybe we will take it a bit more seriously.''
But Dr Laidler says producing the physical evidence is difficult as Rosslyn is a listed building and even the use of metal detectors is banned.
''I have actually pushed very hard to have excavations done, but I have been told it will not be done in the near future,'' he added.
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