As the city of Abydos was founded by predynastic rulers and is famed for its temples such as that of Seti I and its graves, researchers believe the city and cemetery were likely home to high-ranking officials and grave builders.
The antiquities ministry made the announcement about the lost civilisation on Wednesday.
"This discovery can shed light on a lot of information on the history of Abydos," a ministry statement said.
The find could be a much-needed boost for Egypt's struggling tourism industry, which dropped from 14.7 million tourists in 2010 to 9.8 million in 2011 following the uprising that toppled the autocrat Hosni Mubarak.
The bombing of a Russian plane leaving a Red Sea resort with 224 people on board in 2015 was also a crippling setback for the ailing tourism industry.
In the first quarter of 2016, Egypt only registered 1.2 million tourists, which was down one million from the same period the previous year.