A large security force moved in early Wednesday morning to clear the protestors. The activists used social networking sites to call for a fresh wave of demonstrations.
Two protestors and a police officer were killed in Tuesday's demonstrations. Medical officials said a third protester died Wednesday from injuries sustained a day earlier.
The protestors have been inspired by the uprising in Tunisia.
Mubarak, 82, has not said if he plans to run for another six-year term in office.