With little more than a week to go before a parliamentary election that starts the process of transition, the state news agency reported three dead in a second day of violence on Sunday and 192 wounded. Medical sources said four died.
The latest deaths take the overall toll to at least five with more than 1,000 injured.
"The people want the toppling of the regime," thousands of protesters chanted before and after the charge by police backed by military officers who had stayed on the sidelines till then.
The demonstrators accuse the army of seeking to retain power from behind scenes as it oversees the transition, which could see the military remain in control until presidential elections which may not happen until late 2012 or early 2013.
Generals deny any such intention and the cabinet reiterated on Sunday that violence would not delay the staggered parliamentary elections that start on November 28.
The security forces, who moved in as darkness fell, beat some protesters with batons. One group of demonstrators formed a line and bowed in the traditional Muslim prayer, television images showed. Most held their line as the police moved in.
"The army sent soldiers to Tahrir to help state security disperse the protesters. They are beating us hard," said Ragab Shemiekhy, who has been in Tahrir throughout the latest protest.
A Reuters witness saw the dead body of a 28-year-old man on Sunday evening in a makeshift clinic on the edge of Tahrir Square. It was not clear how he had died or if the death was one of those reported by medical sources.
Army police detained dozens of people, a witness said. After initially fleeing, protesters poured back into the square.
"The military council are shutting their ears, they're ignoring us, they don't give a damn about us, and we're going to stay occupying the streets and demanding our rights. Eventually justice will prevail," said Amal El Mohandes, 31.
Egypt's benchmark index tumbled about 2.5 percent on Sunday as investors worried about the outcome of the clashes.
The protest that began on Friday was led by Islamists. But it has since been largely driven by many of the same youthful activists who ended Mubarak's 30-year rule, putting national pride over religion. Some Islamists, including of the biggest group, the Muslim Brotherhood, have since withdrawn.
"Those in the square to do not belong to any party. This is a new scene," Ahmed Abo Barka of the Brotherhood's Freedom and Justice Party told Al Jazeera. "They want to block the route before the Egyptian people who want their election."
The Brotherhood, banned under Mubarak, had tended to take a softer line towards the military than some other groups, which analysts say is to ensure elections go ahead and prevent any return to the kind of repression is suffered in the past.
A row has erupted between political groups and the army-picked cabinet over ground rules for drafting the constitution that could leave the military free of civilian control. Parliament is to pick the assembly to draw up the constitution.
Many Egyptians are angry that nine months after ousting Mubarak, the army remains in charge and police are still using the same heavy-handed tactics against demonstrators.
"We are on the brink of danger. Those asking for the government to fall are asking for the state to fall," Egyptian army General Mohsen Fangary had told a television channel early on Sunday.
He said the election would go ahead on time and the army and Interior Ministry would maintain security. He also said the army, in line with a timetable previously announced, aimed to return to barracks by the end of 2012. Presidential elections could be held by then.
The army-backed cabinet had outraged many Egyptians by presenting proposals for the new constitution that would have shielded the army's budget from civilian oversight and given it a broad national security remit.
It had amended the proposals to give civilian powers more say but this was not enough to prevent Friday's protest.
After a cabinet meeting on Sunday, Deputy Prime Minister Ali al-Silmi said: "We will not back down from the last proposed amendments to the constitutional document."
During streets battles on Saturday night and Sunday morning, police fired round after round of teargas at protesters near the Interior Ministry. Closer to Tahrir the demonstrators laid sheets of metal to block roads into the square.
A security official said police had not used live rounds and had used lawful methods to deal with "troublemakers".
Protests erupted in other cities. About 800 people gathered in front of the security directorate in Alexandria, chanting: "Interior Ministry officials are thugs."
About 1,000 gathered outside a police station in the eastern city of Suez, site of some of the worst violence in the uprising. They threw stones at it and tried to force their way in. Police fired teargas and shot in the air.
Liberal groups are dismayed by the military trials of thousands of civilians and the army's failure to scrap a hated emergency law. Islamists eyeing a strong showing in the next parliament suspect the army wants to curtail their influence.
Analysts say Islamists could win 40 percent of parliamentary seats, with a big portion going to the Muslim Brotherhood.
