An official source said three people were killed and 71 injured in the bloody clashes between the armed forces and protesters in Tahrir Square early on Saturday.
The armed forces stormed the square before dawn to disperse protesters calling for the trials of Mubarak, his family and other corrupt figures from the former regime.
The source told Al-Masry Al-Youm that two soldiers died, and were likely among those who had defied army orders to join the protests.
Interim Prime Minister Essam Sharaf vowed to hold quick investigations in the bloodshed.
Speaking to a privately-owned satellite TV channel Al-Hayat, Sharaf said he is working on securing the release of those arrested during the clashes. Sharaf denied reports that he had submitted his resignation and called on Egyptians to cooperate for a better future.
Security sources told Al-Masry Al-Youm that 42 citizens were arrested on Friday. Among them were three foreigners and others in military uniforms.
