The Egyptian army said Monday that killings outside the Republican Guards House, where Mohamed Morsi is reportedly detained, were provoked by supporters of the ousted president.
Morsi's supporters attacked the premises with live ammunition, the army said.
The health ministry said at least 42 people were killed outside the Republican Guard House in Cairo's Nasr City area, Xinhua reported.
"We dealt with the protesters in the vicinity of the Republican Guard House wisely, while they used live ammunition, Molotov cocktails, stones and others," armed forces spokesman Colonel Ahmed Mohamed Ali said at a press conference.
The military called on all protesters to leave public squares, promising that they would not be legally pursued.
Morsi was ousted by the army last week.
