The attackers seized a number of police helmets and shields, and at least one tear gas gun launchers.
In the same area a small police station was raided and destroyed, and units of riot police were attacked with stones near a police station.
Several thousand demonstrators had previously destroyed with hammers and iron bars a protective wall erected in recent days by the Egyptian authorities before the building where is located the diplomatic mission.
A protester managed by climbing the balcony to pick up the Israeli flag at the top of the building and throw it in the street to the cheers of the crowd.
The demonstrators had earlier attended a rally on the main Tahrir Square, in another part of Cairo, calling for more reforms and democracy to the military who succeeded President Hosni Mubarak, overthrown in February.