The villages date back to the Neolithic era, a period of great development of human technology, beginning about 10,200 BC and lasting until 2000 BC.
This means the settlements were created decades before the time of the pharaohs, which marked ancient Egypt’s golden era.
The Neolithic site was found in Tell el Samara, located some 140km (87 miles) north of the capital Cairo.
This amazing discovery was made by a joint Egyptian and French mission led by chief archaeologist Frederic Gio.
The expedition unearthed several storage silos containing large quantities of animal and plant remains, the Egyptian Antiquities Ministry said in a statement earlier today.
Archaeologists also dug out pottery and stone tools, the ministry added.
The new findings were hailed as a breakthrough by Egypt’s government.
Nadia Khedr, a ministry official responsible for Egyptian, Greek and Roman antiquities on the Mediterranean, said: “Analysing the biological material that has been discovered will present us with a clearer view of the first communities that settled in the Delta and the origins of agriculture and farming in Egypt.”
The items found lead experts to think that humans were already living in the fertile area, in the northern province of El-Dakahlia, as early as 5000 BC.
Scientists’ next step will be to analyse the recovered organic materials and study the different ways in which prehistoric societies lived in the Nile Delta.
In recent years, Egypt has touted archaeological discoveries in a bid to revive tourism after the unrest that followed its 2011 popular uprising.
Earlier this year, experts realised there is an enormous void inside the Great Pyramid of Giza, prompting speculation that there is still a lot to learn about ancient Egyptians.
And last month a second sphinx was found by chance by engineers while carrying out road works.
Describing it as a statue having a “lion’s body with a human head”, the workers soon realised they had made an extraordinary discovery.
Members of the public can now visit the site where the second sphinx was found, Antiquities Minister Khaled al-Anani said.
The greater and more famous Great Sphinx of Giza in Egypt is the largest sphinx in the world, situated on the west bank of the Nile River.
The iconic Sphinx is the oldest known monumental sculpture in Egypt and is commonly believed to have been built during the reign of the Pharaoh Khafre, 2,558-2,532 BC.