Egypt`s military-led interim government declared a state of high alert as police clashed with protesters who raided the embassy building and in the violence one person died of heart attack and 450 were injured, state TV reported.
Protesters torched police trucks and attacked the regional police headquarters after the army intervened to disperse the violent mob who barged into the building housing the Israeli embassy, dumping hundreds of documents out of the windows, tore down the Israeli flag and threw it away.
PTI correspondent in Jerusalem quoting news portal `Ynetnews` said that Israeli Ambassador Yitzhak Levanon, members of the diplomatic staff, their family members and other Israelis sneaked out of Cairo in a special Israel Air Force carrier.
Calling it a secret operation to protect Israelis, the portal said the task was undertaken under tight security and the embassy officials reached the Jewish state this morning.
The attack on the Israeli embassy came suddenly as Egyptians were protesting at the iconic Tahrir Square on Friday, which has become a ritual.
The protesters became restive after a sermon by a Muslim priest who proclaimed, "It would be shame on the Egyptian people if they forget their revolution."
Egypt`s Interior Minister Mansour al-Eissawy declared a state of high alert and the government convened an emergency session to deal with the crisis.
The state TV reported that before leaving Cairo, the Israeli ambassador met with the top General of the ruling military junta and appeared "anxious and even scared".
Levanon had recently returned to Cairo from vacations in Israel as protests raged outside the embassy for the past one month.
US President Barack Obama spoke over phone to Israeli Prime Minister Benjamin Netanyahu, the white House said.
"President Obama expressed his great concern about the situation at the Embassy, and the security of the Israelis serving there," it said in a statement.
"He reviewed the steps that the US is taking at all levels to help resolve the situation without further violence, and to call on the Government of Egypt to honour its international obligations to safeguard the security of the Israeli Embassy," the White House said.
Hours after violence broke out, Egyptian troops and armoured cars marched in to cordon off the entire district housing the Israeli Embassy.
The army intervention came after police reinforcements failed to disperse the mobs. Protesters played cat-and-mouse game with the police throughout the night, amid clouds of tear gas and smoke from the burning tyres.
Thousands crowding outside the besieged embassy jostled to grab the documents thrown outside from the building. The documents in Arabic, English and Hebrew bore the watermarks of the embassy. The Egyptian interior ministry blamed foreign hands for the violence.
An Israeli official said in Jerusalem that the attack on the embassy was a "grave violation of diplomatic norms" and a "blow to peaceful relations between the two nations.