Information Minister Osama Heikal said the country would "take legal measures to transfer those in custody and those who found to be inciting or participating in the events" would be sent to the state security court.
He also vowed Egypt's "total commitment" to protect diplomatic missions on its soil after Israel, the United States and other nations issued statements condemning the attack.
The violence began Friday after a protest in the nation's capital in the iconic center where demonstrations led to the fall of former President Hosni Mubarak.
Sky News reported at least 1,093 people were injured in clashes between police and protesters in Tahrir Square calling for quicker reforms by the transitional government.
The protesters then headed to the Israeli embassy, where they destroyed the newly-built security barrier around the 21-story building housing the embassy. Security forces reportedly did nothing to stop the mob from battering down the wall, according to the Associated Press.
Just before midnight, they succeeded in breaking into the embassy, where they hurled Hebrew-language documents from the windows on to the street below. Egyptian security officers allowed them to do as they pleased, Channel 10 reported.
