David Macmill, 24, was drunk when he pelted the compound in the Red Sea port on Sunday and voiced regret after being arrested, his lawyer said.
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He faces a maximum of four years in jail on charges of "harming the flag or symbol of a friendly country" and "attempting to cause damage with malice", according to the indictment served at Beersheba Magistrate's Court.
"He has no political objective, nor animosity toward the consul," the lawyer, Tamar Olman, said. "It seems as though the Egyptian flag simply caught his eye."
Gunmen described by Israel as Palestinians who had come in through the Egyptian Sinai struck outside Eilat on August 18, killing eight people. Israeli forces killed seven of the gunmen in clashes that also killed five Egyptian border troops.
Egypt threatened to recall its ambassador in protest, and during a rally outside the Israeli embassy in Cairo a demonstrator scaled the building to remove its flag.
The Israeli indictment said that after throwing the first stone and being challenged by two members of staff, Macmill asked them whether the building was the Egyptian mission. When they said yes, he threw two more stones and used foul language.
El-Sayid Nabil, Egypt's vice-consul in Eilat, confirmed that his staff had spotted Macmill stoning the mission and alerted police, who arrested the Israeli. An Egyptian diplomat said there were no injuries in the incident.
Israel has voiced regret for the deaths of the Egyptian personnel last month and Cairo has been mounting security sweeps of the Sinai.
Egypt signed a peace treaty with Israel in 1979. Israel fears Cairo could lose its grip on the desert peninsula after President Hosni Mubarak was toppled in February.
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