The sandstorm brought a giant billboard crashing down on cars, killing one and injuring five, police and witnesses said, The National reported.
There were three other fatalities caused by the storm, which created huge traffic jams in the Egyptian capital and forced authorities to close two Red Sea ports.
Police said another billboard collapsed in Cairo's satellite city of Ramadan 10th, crushing a girl to death. A man was also killed in the Nile Delta province of Menufiyah when a date palm fell on him.
In the Red Sea city of Suez, east of Cairo, a young man fell to his death when he lost his balance while watching the storm from a fourth-floor balcony.
The giant billboard that collapsed in Cairo was located on the October 6 overpass and bridge, a main artery that links the east and west banks of the Nile and snakes through the heart of the city of more than 20 million people, police said.
Police directed traffic away from the bridge, creating bumper-to-bumper traffic across much of the city center for hours.
Separately, footage posted online showed a giant wall of sand moving across the Cairo-Suez desert road, forcing panicked motorists to turn back and dangerously drive against traffic to escape being caught in the storm.
Authorities said they had closed the ports of Suez and Zaitiyat on the Red Sea in the face of 26-knot winds and waves of up to 4 meters high.
Sandstorms known as Khamasin are common in Egypt during spring and early summer, but storms of this magnitude are rare.
SKH/PR