The storming of the Israeli Embassy by a mob of Egyptian protesters inflicted a "severe injury to the fabric of peace" between the two countries, Israel's Prime Minister Benjamin Netanyahu warned Saturday.

But he said Israel "will continue to stand by the peace treaty with Egypt" and will work with the government in Cairo to get its ambassador and diplomatic staff back to the capital as soon as possible.  

The ambassador and the entire embassy staff except for one deputy ambassador were evacuated from Egypt along with their families in the face of the overnight rampage at the Nile-side embassy in Cairo, when hundreds of protesters tore down a concrete security wall outside the building, set fires in the street and dozens broke into an office of the embassy tossing documents off the balcony to the crowd below.

Rioting that extended into the pre-dawn hours significantly added to the already growing tensions between the two Mideast neighbours, seven months after the ouster of Egyptian President Hosni Mubarak. Many in Israel fear that this year's uprisings around the Arab world are giving freer rein to anti-Israeli sentiment.

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Protesters outside the Israeli Embassy in Cairo gather as tear-gas smoke rises nearby during clashes with Egyptian security early Saturday. (Khalil Hamra/AP)

The Egyptian government promised to send those who incited or took part in the violence to an emergency state security court, the Reuters news agency reported.

Later on Saturday, Egyptian troops clashed with dozens of protesters, trying to push them away from the Israeli Embassy. Troops used batons to disperse the crowd.

Netanyahu tempered his remarks about the rioting and praised Egyptian authorities for rescuing six embassy personnel who were trapped by the rioting.

The six staffers — apparently a security detail in offices that were otherwise empty — had taken shelter in a room in the embassy and at one point there was only a single wall between them and protesters who were ransacking offices, Netanyahu said.

Egyptian commandos eventually made their way in and got them out, he said.

"However, Egypt must not ignore the severe injury to the fabric of peace with Israel and such a blatant violation of international norms."

Ties thin

Mubarak was a close ally of the Israelis, building economic ties and co-operating with them on security — particularly helping the Gaza Strip. Since his Feb. 11 fall in the face of unprecedented protests, ties between the two countries have steadily worsened as Egypt's new military rulers ease off his pro-Israeli policies in the face of their widespread public unpopularity.

Anger increased last month after Israeli forces responding to a cross-border Palestinian militant attack mistakenly killed five Egyptian police officers near the border. The militants, apparently from Gaza, had trekked across Egypt's Sinai Peninsula and sneaked into Israel, killing eight Israelis.

At the time, Cairo protesters demanded the expulsion of the Israeli ambassador and calls grew in Egypt for ending the historic 1979 peace treaty with Israel, a pact never supported by ordinary Egyptians.

Netanyahu said Saturday that Israel will respect that deal, which saw as being "in both countries' interest."

3 killed in protests

The Egyptian Health Ministry said three people were killed and more than 1,000 people hurt during the street clashes between the protesters and police that began after midnight and lasted until nearly 6 a.m. Saturday. Nineteen protesters were arrested.

Police and army troops fired tear gas and shot live ammunition in the air trying to disperse the crowd of thousands, as cars, police vehicles and trees on the streets were set ablaze.

Saturday morning, the streets around the embassy were littered with debris, shattered glass and rocks. Dozens of police vehicles lined up the streets leading to the embassy and the nearby police headquarters in Giza. Several charred bodies of private cars sat motionlessly on side streets, with some still smoldering.

Black clad anti-riot police backed by army troops and their armoured vehicles were deployed in large numbers in streets surrounding the embassy.

The unrest began Friday afternoon when hundreds of protesters tore down a concrete security wall that Egyptian authorities had recently erected outside the embassy building in reaction to the repeated protests there. For hours, young men battered the wall with sledgehammers, ripping off chunks with their bare hands.

The Israeli ambassador, Yitzhak Levanon, his family and nearly all the staff and their dependents — some 80 people — were flown out of the country by military aircraft overnight, according to an Israeli. Only the deputy ambassador was still in Egypt.

Mustafa Sayid said he was among the group of protesters who broke into the embassy. He showed a reporter cellphone video footage he said he recorded inside of young men ransacking the room.

The group got into the building through a third-floor window and climbed the stairs to the embassy. They worked for hours to break through three doors to enter the embassy, said the 28-year-old man. They encountered three Israelis and beat one of them.

During the rioting, U.S. President Barack Obama assured Netanyahu the U.S. was acting "at all levels" to resolve the situation. Netantayu thanked Obama for help at a "critical moment" and said the American assistance was "a relfection of the special relationship between Israel and the U.S., which is especially important in these days."

With files from CBC News