Egypt's ruling military council imposed an overnight curfew in the area around the defence ministry in Cairo after one soldier was reported killed and hundreds wounded in clashes there.
Soldiers used water cannons and tear gas against protesters on Friday.
Dozens of people were arrested. Protesters later dispersed and some joined a protest in Tahrir Square.
On Wednesday, unidentified assailants attacked protesters outside the ministry, leaving at least 20 dead.
The protesters, who were demonstrating against the ruling Supreme Council of the Armed Forces (Scaf), accused the government of orchestrating the attack.
The curfew was in force from 23:00 to 07:00 (21:00 to 05:00 GMT)
The BBC's Jon Leyne, who was at Friday's demonstration, said trouble flared when protesters ignored army warnings not to approach the ministry.
They tried to break through a protective ring of barbed wire and soldiers responded with water cannons and tear gas.
Both sides threw rocks at the other in clashes that lasted several hours.
Later the health ministry said one soldier had been killed and about 300 people wounded. It says about 130 are being treated in hospital.
The army says proceedings against those arrested have already started in military courts.
The unrest comes just three weeks before presidential elections are due to be held - the first since Hosni Mubarak was forced to step down.Islamists blamed
Earlier on Friday, thousands once again gathered in Tahrir Square - the focus of the uprising that ousted President Hosni Mubarak in February 2011 - to protest against the Scaf.
The crowd expressed their anger at the generals' failure to protect the demonstration on Wednesday and reiterated the demand that they hand over power to a civilian administration immediately, rather than after the presidential election.
In the afternoon, protesters began walking from Tahrir Square to the defence ministry in the capital's Abbasiya district.
The protesters started throwing stones and clashes then broke out.
State television blamed the Muslim Brotherhood for the trouble, despite the fact that the Islamist movement has been urging its supporters to stay away.
Clashes also occurred between protesters and security forces in Egypt's second city of Alexandria on Friday.