The human remains were discovered upon renovations to the cellar of the Monoprix supermarket at Réaumur-Sébastopol, near the centre of the capital.
French law stipulates that buildings in certain historic locations can be subject to archeological assessments before renovations, and the Culture Ministry recommended the site for investigation.
"We suspected there was something, but we didn't expect so many corpses," Marie-Christiane Casala, director of France's National Institution for Preventive Archeological Research for the Paris region, told RFI.
Casala explained the most striking archeological feature of the corpses is the manner in which they were buried.
"What is unusual is the corpses are very tight," indicating the burials happened hastily, Casala said. But she added that archeologists are limited in what they can determine for the time being.
"We can say two things: they were poor people, and they died from a disaster," Casala explained. "We do not know for the moment if it was disease, or if it was due to a war, or something else."
The building that houses the Monoprix was built for another grocery in the 19th century. It sits on the site of Trinity Hospital, which was founded in 1202 and which opened a cemetery at the height of the Black Death plague epidemic in 1353.
The cemetery operated until the 18th century, but Casala says it is impossible to determine the dates and causes of death until the remains are removed for laboratory analysis.
In the meantime, the supermarket remains fully operational throughout the excavation, which began in January.
"The only impact is that we will be there for two or three more weeks before they can begin the renovation of their cellar," Casala said.
The bones will be removed and analysed over the coming months before being put into storage.
"They are property of the state," Casala said. "There are different places around Paris where we keep with the state, bones or everything we find in archeological excavations."