Israel airlifted its ambassador home and sought U.S. intervention with Egypt to help secure its embassy here early Saturday, hours after thousands of Egyptian protesters besieged the building, with several managing to gain entry and fling Hebrew-language documents from a balcony.

Protesters knocked down a 12-foot concrete wall that had been built last week to protect the embassy, which is near the top floor of a 21-story residential building in the upscale Dokki area. At least two protesters scaled the front of the building to pull down the Israeli flag, hanging from the 20th floor. It was the second time in recent weeks that demonstrators had removed the flag.

The crowd burned Israeli flags and threw rocks at security forces as protesters denounced the killing of five Egyptian border guards last month. The guards were killed as Israeli troops pursued militants who had crossed from Egypt’s Sinai Peninsula and carried out a deadly attack north of the Israeli resort town of Eilat.

Late Friday, protesters appeared to have reached the embassy’s foyer, throwing documents from a balcony, said an Israeli official quoted by Reuters news agency. It was not clear whether the documents were sensitive. Egyptian security forces used tear gas and sent a string of armored personnel carriers to try to clear away the protesters.

Egyptian Deputy Health Minister Hamid Abaza told the Associated Press that at least three people died and more than 1,000 were hurt during the street clashes with police. Earlier, the state-run Middle East News Agency said that 448 people were injured in the fighting around the embassy, including 46 police officers.

In Israel, Prime Minister Benjamin Netanyahu called the incident, which led to the departure of the Israeli ambassador and nearly all of his staff, a serious breach of bilateral relations. 

“The fact that Egyptian authorities ultimately acted with determination is laudable,” Netanyahu was quoted as saying by an official in his office. “That said, Egypt cannot conduct business as usual after this harsh blow to the fabric of relations with Israel and gross violation of international norms.”

Israeli officials who tracked events during the night described tense hours during which Netanyahu spoke by phone with President Obama to seek help in protecting the embassy and extricating six Israeli security guards trapped inside when a mob broke through an outer door into the public reception and consular affairs area. The ambassador and other embassy staff were not in because it was Friday night, the Jewish Sabbath, and a day off in Egypt, when the embassy is closed.

Netanyahu was also in contact with the Egyptian chief of intelligence, Gen. Murad Muwafi, a member of the ruling military council, according to the officials. Defense Minister Ehud Barak meanwhile, spoke to U.S. Defense Secretary Leon Panetta and with Dennis Ross, the president’s Middle East adviser on the National Security Council, his office said in a statement early Saturday. The statement said Barak had asked Panetta and Ross “to protect the embassy from the demonstrators who broke into it,” but Israeli officials later clarified that to say that the request was for the Americans to press the Egyptians to take action.

A senior Pentagon official said Panetta spoke Friday evening with Barak and the head of Egypt’s ruling military council, Field Marshal Mohammed Hussein Tantawi, to try to ease the crisis. Tantawi told Panetta that Egypt would take necessary measures to secure the Israeli Embassy, the senior Pentagon official said.

“The rioters were literally a door away” from the security guards, said one Israeli official, who spoke anonymously in order to talk freely.  “There was very real concern for their safety and their lives. The prime minister spoke to them directly because he moved during the night to a situation room in the Foreign Ministry, where there is a direct link to the embassy. It was a very grave incident, and we were very concerned that it was going to get worse.”

After tear gas was used to disperse the protesters, the Israeli guards were eventually extricated at about 5 a.m. Saturday by Egyptian commandos and escorted to the airport, where they were flown back to Israel on an Israeli air force plane, according to the Israeli officials. Another Israeli plane left earlier carrying the ambassador, Yitzhak Levanon, the embassy staff and their families — about 80 people in all, the officials said.  

The deputy ambassador, Yisrael Tikochinsky-Nitzan, remained in a “secure location” in Cairo to maintain contact with the Egyptian authorities, said the official who spoke anonymously. He added that “we know” that American intervention with the Egyptian authorities helped “stabilize the situation and get our people out.”

The area around the embassy was a tense scene of destruction Saturday, with hundreds of security forces massing in the streets around the building, occasionally rushing out with upraised batons to push people back, then regrouping. Six charred police trucks reeking of burnt rubber lined the alley behind the embassy block.

One soldier said that the security forces had taught protesters “a lesson” Friday night when they repelled people with tear gas and, according to some witnesses, rubber bullets. They appeared to be administering the same lesson again Saturday, as shouts of pain and the sound of blows rang out from behind a tall wall at a nearby school building.

Diplomats in Cairo voiced concern, wondering whether their own embassies were secure.

“When you wind up with the whole mission fleeing the country, that’s a very bad situation,” said one Western diplomat, who spoke on the condition of anonymity to candidly discuss internal deliberations. “I’m sure all embassies will be discussing evacuation plans now. You storm one embassy, that makes everybody nervous."

The Egyptian Interior Ministry has put police on high alert, and Prime Minister Essam Sharaf has summoned an emergency meeting of his cabinet, according to the state news agency.

Anger toward Israel has united Egyptian protesters like nothing else. Thousands returned to Tahrir Square on Friday calling for a faster transition to civilian rule, in the largest demonstration since activists canceled a sit-in at the beginning of August. But the gathering in Tahrir — in which disparate groups clustered separately, each pressing their own issues — lacked the energy of the evening confrontation at the embassy, which developed after protesters broke away from the square and marched the two miles to the mission.

“We are here to protest against the bad behavior of the Israelis,” said Sheidi Abu Sheidi, 24, a student. “Our soldiers were killed on the border, and we had hoped that the Egyptian army would do something. It didn’t happen, so we had to come here and say no.”

The crowd was chanting a variation on a slogan from the 18 days of protests against Mubarak: “The people demand the removal of” — instead of Mubarak — “the ambassador.”

Friday’s gathering, which organizers called “Correcting the Path,” was intended to pressure Egypt’s military rulers to provide a timeline for ceding power to civilian control, after months in which elections have been proposed and then postponed.

Parliamentary elections are set for November, with a presidential election to follow, but no dates have been set for either vote.

Protesters also called for an end to military trials of civilians, which have continued unabated since longtime president and former military general Hosni Mubarak was ousted Feb. 11, after weeks of massive but peaceful civilian protests.

“Mubarak’s men are still in control, and we can’t do anything about it,” said Mohammed Saad, 24, a student at al-Azhar University, Egypt’s preeminent Islamic school. “The poor are still poor, and the children of the rich are the only ones getting jobs.”

Tahrir Square, the heart of bustling Cairo, has been the center of Egypt’s political unrest. Hundreds of protesters were killed there in January and February — deaths for which Mubarak is now on trial.

Liberal Facebook activists have gathered there repeatedly since Mubarak’s departure in an attempt to make their voices heard. Islamic groups have come to show their strength and organization. From time to time, the army has swept them all away in clashes that show it is still the force in power.

Military security forces and riot police have clashed with protesters at previous demonstrations, but this week the army issued a statement saying it would allow peaceful gatherings Friday as long as no property was damaged.

And after weeks under tight military control, Tahrir Square appeared to have no security presence Friday.

Instead, protest organizers in street clothes checked identification at entrances to the square.

Despite thousands of protesters, the square was less than half full, and one important group was glaringly absent: Islamic fundamentalists, who have emerged as a powerful political force since Mubarak stepped down.

Once outlawed, the Muslim Brotherhood now can hang its campaign signs everywhere, and Cairo is speckled with them. Salafists — adherents to a puritanical, conservative form of Islam — also can operate far more openly than they once did. But the Brotherhood’s political party, called the Freedom and Justice Party, and the Salafists had announced before Friday’s protest that they would not participate.

Their absence was a marked difference from a much larger protest in late July, when tens of thousands of mostly Salafist protesters packed Tahrir Square to resist what they saw as attempts by the military and liberal protesters to enact constitutional changes that would enshrine Egypt as a secular state.

The July gathering demonstrated the highly organized Islamic groups’ ability to turn out a crowd. Friday’s event revealed the liberals’ relative weakness in that area, a combination that could have important electoral consequences in the November parliamentary elections.

The uncertainty surrounding politics in Egypt extends to whether Mubarak will be convicted on charges of corruption and complicity in the deaths of protesters. On Sunday, Mohammed Hussein Tantawi, the country’s de facto head of state, is scheduled testify in a closed courtroom about Mubarak’s actions during the January and February protests. Many in Tahrir on Friday were skeptical that Tantawi would implicate his former boss.

“We all hope that he will testify against him,” said Mohammed Yusef, 25. Whether that will actually happen, he said, is another question.

Hassieb is a special correspondent. Correspondent Joel Greenberg in Jerusalem, staff writer Craig Whitlock in Washington and special correspondent Muhammad Mansour in Cairo contributed to this report.