Network Rail engineers discovered the small cave, with marks and evidence of use in the 14th century, while stabilizing the embankment between the railway line and the A3100 Old Portsmouth route.
The sandstone cave is made up of several sections ranging from 0.3 meters to about 0.7 meters high and is believed to be the surviving section of a much larger cave.
The rest may have been lost when the railway line was cut into the hill in the early 1840s.
The first discoveries of a specialized archaeological contractor suggest that it was a medieval sanctuary or a later hermitage associated with the Sainte-Catherine chapel of the early 14th century, the ruins of which are located on the nearby hill.
It may even have earlier origins as a site of cult activity, because of its name from Drakehull, or “dragon hill” dating back to before the 14th century.
The images taken on the site show the presence of a Gothic niche decorated with dots with a Calvery cross nearby.
There are seven or eight other niches, and experts have found considerable evidence of writing and other markings through the ceiling of the cave.
The cave is partially covered with black dust deposits, which are said to be lamp soot. The remains of two alleged fire wells were also found in the cave floor.
The hope is that radiocarbon dating can be used to establish the period during which the cave was in service.
Mark Killick, Director of Routes for Network Rail Wessex, said: “This is an unexpected and fascinating discovery that helps to visualize and understand the rich history of the region.
“A complete and detailed recording of the cave has been made and every effort will be made to preserve the elements when possible during the reclassification of the delicate and vulnerable sandstone cut. “
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Tony Howe, director of historical environmental planning and archaeologist for the Surrey County Council, added: “The discovery of this cave is extremely exciting. It is very early in the process of understanding its full meaning, but the potential for knowledge acquisition is enormous.
“We look forward to learning a lot more on the site as the studies progress. “