The protesters, who were mostly students from the University of Aden, "vandalised furniture before they were removed peacefully from the building", the official said on Tuesday, asking not to be identified.
Another security official said three staff members were inside the building at the time but they were unhurt.
The official said one protester was wounded when a consular guard opened fire and that the protesters retaliated by setting fire to two consular vehicles.
More than 20 demonstrators were arrested.
Protests have been held across the Middle East against the four-day-Israeli air attack on Gaza, which has killed at least 360 Palestinians and wounded more than 1,600.
Many Arabs have accused Cairo of giving the green light to Israel's assault after Hosni Mubarak, Egypt's president, hosted Tzipi Livni, Israel's foreign minister, for talks just two days before the launch of the onslaught.
In the absence of Israeli embassies in most Arab capitals, Egyptian diplomatic missions have been a particular focus of the demonstrations.Read More