Soldiers used water cannons and tear gas outside the defence ministry.
Dozens of people have been arrested and a night-time curfew is now in force. 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 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.
Earlier on Friday, thousands once again gathered in Tahrir Square - the focus of the uprising that ousted President 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, several kilometres to the north-west.
The protesters started throwing stones and clashes then broke out.
At one point, soldiers broadcast a message on loud-hailers saying the defence ministry would only be stormed over their dead bodies, and that reinforcements were on the way.
A senior general later appeared on television to announce a night-time curfew around the defence ministry.
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 happened between protesters and security forces in Egypt's second city of Alexandria on Friday.
Source: BBC News
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