Information Minister Osama Hassan Heikal made the announcement in a televised statement after Israel, the United States and other countries criticized the storming of the building.
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Egypt will "take legal measures to transfer those in custody and those who are found to be involved in inciting or participatig in (Friday's) events to the emergency state security court," the minister said after a meeting of a ministerial crisis group and talks with Egypt's military ruler.
Heikal also expressed Egypt's "total commitment" to the protection of diplomatic missions on its soil, saying that "Egypt affirms its full commitment to respect international conventions, including the protection of all diplomatic missions."
Earlier on Saturday, Egyptian Prime Minister Essam Sharaf has offered to resign Saturday along with his cabinet ministers over the failed handling of Friday's protests in Cairo, sources close to the cabinet told government-owned newspaper al-Ahram.
However, Egypt's Higher Military Council rejected his resignation, al-Arabiya network reported.
The governor of the Cairo district where the Embassy is located said Saturday that the wall, which has been completely demolished by protesters overnight, will not be reconstructed, adding that instead the premises will be secured with the necessary means.
The governor also noted that he has handed a detailed report on the riots to the prime minister, in which he committed to return to normal activity within 12 hours.
Some 4,000 people demonstrated outside the Israeli Embassy in Cairo on Friday evening, tore down the wall set up to defend the diplomats, removed the Israeli flag from the building and clashed with security forces. Three protestors were killed and more than 1,000 were injured.
Dozens of protestors stormed the embassy building, where six security guards and workers were stranded. The rioters threw Israeli documents out of the windows and reportedly beat up one of the employees.
Protestors storm Israeli Embassy building (Photo: EPA)
The six Israelis were evacuated from the embassy by an Egyptian commando force early Saturday, and returned to Israel. Ambassador Yitzhak Levanon, some 80 diplomats, their family members and other Israelis residing in Cairo were flown back to Israel earlier. The deputy ambassador remained in the Egyptian capital to maintain the embassy.
Sharaf was appointed prime minister on March 3, after the revolution which led to President Hosni Mubarak's downfall. Sharaf enjoyed the citizens' support but his government began drawing criticism recently.
According to recent reports, several years ago, when he served as minister, Sharaf gave his associates official roles.
Bahrain slams Egypt
Friday's protests were not just against Israel, but also against the Military Council controlling Egypt. Sharaf convened his cabinet for an urgent meeting Saturday morning. At the same time, the Interior Ministry said it put police on high alert and canceled all police holidays.
Meanwhile on Saturday, Israel received surprising support from Bahrain's foreign minister, Sheik Haled bin Ahmad bin Muhammad al-Halifa, who condemned the attack on the Israeli Embassy in Cairo.
The minister wrote on his Twitter page that "the failure to defend the embassy building is a blatant violation of the 1961 Vienna Convention on Diplomatic Relations."
European governments also denounced the attack; British Prime Minister David Cameron urged both countries to work together in order to calm tensions and maintain regional stability, while German Foreign Minister Guido Westerwelle issued a condemnation, saying that Germany "expects the Egyptian authorities to protect the embassy in accordance with international commitments and avoid any further escalation."
Attila Somfalvi, Ronen Medzini, AFP and Reuters contributed to this report
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