According to a report in the Telegraph, the pagoda was wedged tightly inside an iron case that was discovered at the site of a former temple in the city in August this year.
The four-storey pagoda, which is almost four feet high and one-and-a-half feet wide, is thought by archaeologists to be one of the 84,000 pagodas commissioned by Ashoka the Great in the second century BC to house the remains of the Buddha.
It matches a description of another of Ashoka's pagodas, which used to be housed underneath the Changgan Buddhist temple in Nanjing.
A description of the contents of the pagoda indicate the presence of a gold coffin bearing part of Buddha's skull inside a silver box.
Although scans have confirmed that there are two small metal boxes inside the pagoda, experts have not yet peered inside.
According to Qi Haining, the head of archaeology at Nanjing Museum, "This pagoda may be unique, the only one known to contain parts of Buddha's skull".
But he said there would be a lengthy process before the cases could be opened.
"The discovery of the relic will have a huge influence on the cultural history of Buddhism in China and will establish Nanjing as a premier site. It will be a great encouragement for Buddhists as well as for future studies," said De Qing, an expert in Buddhism in Nanjing.
"It is important for Buddhism as a religion to have these sarira, or relics, to show its followers. The more a Buddhist practises, the more relics will remain of him after his death. I am hugely excited. I think they should take the skull outside of the container, it is a sacred item, but it is not an untouchable item," he added.
Siddhartha Gautama, who is believed to have been born in the fifth century BC, was a spiritual teacher and recognized by Buddhists as the Supreme Buddha of our age.
Also known as Shakyamuni, or the Sage of the Sakyas, his teachings are contained in the Tripitaka, the canon of Buddhist thought.