Six tanks and two armored vehicles belonging to the Republican Guard were stationed at roads leading to the palace in the upscale Cairo district of Heliopolis. The guard's commander, Maj. Gen. Mohammed Zaki, sought to assure Egyptians that his forces were not taking sides.
"They will not be a tool to crush protesters and no force will be used against Egyptians," he said in comments carried by the official MENA news agency.
Several dozen anti-Morsi protesters continued to demonstrate across the street from the palace past the military's afternoon deadline, chanting slogans against the president. Thousands marched through Cairo toward the palace and joined the protest Thursday evening.
"We raise Egypt's flag but they raise the Brotherhood flag. This is the difference," protester Magdi Farag said as he held the tri-colored national flag stained with blood from his friend's injury in clashes the night before.
"We will not leave until he leaves," Farag said about the president.
Brotherhood supporters outside the palace accused opposition protesters of being Mubarak loyalists or foot soldiers in a coup attempt.
"They want to take over power in a coup. They are conspiring against Morsi and we want him to crack down on them," said one, Ezzedin Khoudir. "There must be arrests."
Outside the president's house in his hometown of Zagazig, about 80 kilometers (50miles) north of Cairo, police fired tear gas to disperse hundreds of protesters who had gathered, security officials said.
Egypt has seen sporadic clashes throughout nearly two years of political turmoil after Mubarak's ouster in February 2011. But this was by far the worst violence between segments of the public.
The violence began when the Brotherhood called on its members to head to the presidential palace to stand up against what a statement termed as attempts by the opposition to impose its will. The group called on their supporters to "protect legitimacy after an infringement by a group the night before that imagined it could shake legitimacy or force its will on people."
Thousands of Brotherhood members and other Islamists then descended on the area Wednesday afternoon, chasing away some 300 opposition protesters who had been staging a peaceful sit-in outside the palace's main gate a day after tens of thousands converged outside the palace to denounce the president.
Clashes later ensued, with the two sides using rocks, sticks and firebombs. Riot police were deployed to intervene.
The Muslim Brotherhood were chanting "as if they are in a holy war against the infidels," businessman Magdi Ashri said of the clashes. Protesting outside the palace again Thursday evening, Ashri said that he was once a supporter of the president, but after last night has changed his position.
The Brotherhood also said three of its offices outside Cairo were torched by protesters Wednesday.
Unlike Mubarak, Morsi was elected in June after a narrow victory in Egypt's first free presidential elections. But many activists who supported him have jumped to the opposition after his Nov. 22 decrees and the rushed constitution drafted by his Islamist allies despite a walkout by minority Christian and liberal factions.
The Health Ministry said six people were killed and 644 injured by beatings, gunshot wounds and tear gas inhalation. The Brotherhood said all those killed were their supporters, but the claim could not be immediately verified.
A journalist for the independent daily Al-Fagr newspaper was in critical condition after being shot in the head with a rubber bullet, according to a staff member who spoke to The Associated Press on condition of anonymity in exchange for releasing the information ahead of a formal announcement. The newspaper said it did not know who fired the rubber bullet.
Associated Press writer Aya Batrawy contributed to this report.
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