Police were trying to prevent protesters from reaching the Interior Ministry building while protesters were trying to stop police from reaching the square, Haaretz reported.
The New York Times reported army troops replaced police and cement barricades were placed behind a line of coiled barbed wire to separate protesters from the ministry building.
At least 38 people died and hundreds were wounded since the violence erupted late last week.
Egypt's military rulers apologized Thursday for the killing of protesters in Cairo's Tahrir Square.
"The Supreme Council of the Armed Forces presents its regrets and deep apologies for the deaths of martyrs from among Egypt's loyal sons during the recent events in Tahrir Square," a statement on the council's Facebook page read. "The council also offers its condolences to the families of the martyrs across Egypt."
Both sides threw stones at each other Thursday, but one protester told Haaretz police were shooting live ammunition.
"The police are also shooting metal bullets and some protesters have already lost their eyes from this," protester Husam Said said.
Witnesses said Defense Minister Field Marshal Hussein Tantawi, leader of the military council that took power when former President Hosni Mubarak was ousted in February, was the focus of the protests and chants calling for his removal were heard among the demonstrators.
The confrontations Wednesday drew international calls action to end the violence, the Times said.
The French Foreign Ministry condemned "the excessive use of force against demonstrators," the Times said. Navi Pillay, the U.N. human rights chief, called for an independent investigation.