The UN has condemned the excessive use of force by the army and police, at least 10 people being killed in the violence since Friday.
The United States, for their part expressed their deep concern.
The violence occurred between the two rounds of the second phase of parliamentary elections.
Freedom and Justice party (CLE), an offshoot of the Muslim Brotherhood politics, won about 40% of the votes in the first round of the second phase last week, said with the CLE on Sunday.
During the night, police and soldiers armed with clubs came to evict the demonstrators in Tahrir Square, the epicenter of the uprising that led to the overthrow of Hosni Mubarak in February, said a Reuters reporter.
The protesters fled into side streets, away from sensitive areas such as the approaches to the parliament, the seat of government and the Ministry of the Interior. They were previously on revenues up after having been deported once.
“Down Tantawi,” chanted the demonstrators Sunday evening, pointing to the Marshal Mohamed Hussein Tantawi, Minister of Defence of Hosni Mubarak for 20 years and now head of the Supreme Council of the Armed Forces (AFSC) overseeing the transition.
Young men hurled stones and Molotov cocktails against the police, in which the police seem to have replaced the military front line.
Secretary of State Hillary Clinton said he was “deeply concerned” by the violence in Egypt. “I urge the Egyptian security forces to respect and protect the universal rights of all Egyptians, including the right to assemble and the right to express his opinions freely and peacefully,” she added.