Rival demonstrations of supporters and opponents of the military-backed government took place in Cairo yesterday.
But police quelled anti-government protests, and arrests were reported in Cairo and Alexandria as violence broke out.
Forty-nine people were killed, the ministry said, in 24 hours of fighting across Egypt as police and supporters of the military-installed government clashed with Islamist backers of president Mohamed Morsi, who was deposed in July after a single turbulent year in power.
Hundreds have died since July when the army deposed Morsi, the country's first democratically elected president of the Muslim Brotherhood.
More From This Section
Extra security measures were in place yesterday as Egyptian Interior Minister Muhammad Ibrahim urged Egyptians not to be afraid to go to events marking the anniversary of the uprising.
Thousands of supporters of the military and the government gathered in high-profile locations including Tahrir Square - the focal point of the 18-day popular revolt in 2011, the BBC reported.
Meanwhile yesterday, an army helicopter crashed in the restive Sinai peninsula, with an unconfirmed report that it was shot down by militants, killing its crew of five soldiers.
A large car bomb exploded near a police building in Suez, at the southern entrance of the Suez canal, with reports that nine people were injured.
At least 18 people died in violence on Friday.
Three years on from an uprising that raised hopes of political reform in the Arab world's most populated country, rival demonstrations are showing the deep divisions.