This is mainly due to differing interpretations of the Gospels.
The Gospel of John describes the trial of Jesus taking place near a gate and uneven pavement, which some archaeologists, including Shimon Gibson, an archaeology professor at the University of North Carolina at Charlotte, believe matches evidence at the site.
'There is, of course, no inscription stating it happened here, but everything - archaeological, historical and gospel accounts - all falls into place and makes sense,' he said.
The Reverend David Pileggi, minister of Christ Church located nearby the museum, told the newspaper that the discovery confirms 'what everyone expected all along, that the trial took place near the Tower of David.'
However, not everyone is convinced. Some experts say that the Gospel's use of the word 'praetorium' - which means general's tent in military barracks in Latin - suggests the pivotal trial took place in the Antonia Fortress.
The fortress lies in the north eastern part of the old city, near Temple Mount.
Despite some uncertainty, it's thought that the prison will become a visit on the pilgrim trail.
Eilat Lieber, Director of the Tower of David Museum, says the museum is working with tour guides to explain the history and significance of the remaining ruins.
However, Reverend Pileggi doesn't think that the prison will become a major site of pilgrimage.
'What makes a place holy is the fact that people have gone there for hundreds of years, prayed, cried and even celebrated there, so I don't think there will be changes to the route anytime soon,' he said.