The Matariya archaeological site at Cairo University on Tuesday has been cleared of rubble and construction materials by the Tourism and Antiquities Police.
A mud brick wall, the foundations of houses, and materials used in the construction of new properties was removed from the area around King Merneptah's pillar.
The site was once a major religious centre in ancient Egypt.
“This is the first step in a long series of attempts to end all encroachment on archaeological sites and monuments throughout the country,” Antiquities Minister Mohamed Ibrahim said.
Security would also be improved, he added.
Over the last year a lack of security measures at archaeological sites in Matariya, Boulaq and Ezbet Kheirallah among others have led to encroachment.