Two people have died in clashes in Fayoum on Friday between security forces and supporters of ousted president Mohamed Morsi, reported Al-Ahram's Arabic website. Another person was killed in clashes in Cairo, confirmed the health ministry.
Twenty-three people were injured in the two locations, according to the ministry.
The protests started after Friday prayers.
Friday protests have been common since Morsi’s ouster last July, despite a law issued in November which criminalises unauthorised public demonstrations.
Morsi’s ouster has also led to a spike in militant attacks. They were initially concentrated in the Sinai Peninsula, but in recent months they have become frequent in the Nile Delta region and the capital.
The National Alliance to Support Legitimacy, an Islamist coalition that supports ousted Muslim Brotherhood president Mohamed Morsi, has called for protests to coincide with next week's presidential election.
A conservative estimate puts the death toll since Morsi's fall at well over 1,500 people, mainly Brotherhood supporters. About 500 police and soldiers have been killed in bombings and shootings.