Three people were killed and 1,049 were wounded in the clashes that began on Friday and raged into the early hours of Saturday around the tower block housing the embassy, the Health Ministry said.RELATED:Timeline of Israel embassy attack in CairoEgypt forces extract Israeli security guards from embassy“Egypt witnessed a harsh day that inflicted pain and worry on all Egyptians. It is clear that the behavior of some threatens the Egyptian revolution,” Information Minister Osama Hassan Heikal said.Egypt would transfer those in custody or “involved in inciting or participating in [Friday’s] events to the emergency state security court,” he said, adding that Cairo would use emergency laws still in place to protect the nation.“This was meant to be a day of protest against the way the country is ruled, and instead all of the attention was shifted to the people who went to the Israeli Embassy,” Khairi Abaza, a senior fellow at the Washington-based Foundation for Defense of Democracies, told The Jerusalem Post. “Egypt’s new rulers need to explain to the Egyptian people the reality of the treaty with Israel and the consequences of such actions.“What do we expect after one of the military commanders goes to speak with the guy who removed the Israeli flag from the embassy a few weeks ago, and treats him like a hero?” said Abaza, who was raised in Cairo and visits often. “How can you honor someone who breaks the law?” On August 20, a man scaled the embassy building, took down Israel’s flag and replaced it with Egypt’s. Protests continued daily, but did not turn violent until the latest flare-up.In response to the protests, the authorities had erected a wall around the building, which was quickly defaced with anti-Israel slogans and then painted in Egypt’s national colors.On Friday, the wall was torn down after a demonstration in Cairo’s Tahrir Square calling for speedier reforms and a deeper purge of officials who worked for Hosni Mubarak, the former president on trial on charges including conspiring to kill protesters.Protesters lit tires in the street and at least two vehicles were set alight near the embassy. Many had come from a demonstration earlier on Friday in central Cairo calling for the army to end emergency law and speed up other reforms.“Our dignity has been restored,” said Mohi Alaa, 24, a protester near the site of the overnight clashes, told Reuters. Bits of concrete and bullet casings were strewn over the street. “We don’t want the Americans’ money,” he said.Some 500 protesters stayed after dawn and a few threw stones at police, who gradually pushed them away and secured the area around the embassy, located on the upper floors of a residential block overlooking the Nile.It was the second big eruption of violence at the embassy since five Egyptian border guards were killed on August 18 when Israeli forces shot at terrorists who had crossed from Gaza, via Egyptian territory, into Israel and killed eight Israelis near Eilat. Egypt then briefly threatened to withdraw its envoy to Israel.Israel has stopped short of apologizing, saying it is still investigating the Egyptian deaths.The information minister’s statement followed a crisis meeting between Prime Minister Essam Sharaf and other ministers, as well as talks with Field Marshal Mohamed Hussein Tantawi, who heads the military council that has ruled Egypt since Mubarak resigned on February 11. State television said the military council rejected Sharaf’s offer to resign.Some Egyptian politicians and activists criticized the violence, even if they backed the anti-Israel demonstration.Presidential candidate Hamdeen Sabahy called for the army to take a “serious stance matching the public anger” toward Israel but said violence sullied the image of Egypt’s uprising.“The treaty preserves a fragile peace, and it’s something that has to be preserved at any cost,” Abaza told the Post. “Conflict between the two countries is a loss for both, and there is no reason for a military conflict or for canceling the treaty. What would Egypt or Israel get out of that?” Reuters contributed to this report.