The eruption of violence, which began Saturday, reflects the frustration and confusion that has mired Egypt's revolution since Hosni Mubarak fell and the military stepped in to take power.
Nearly 1,800 people have been injured since demonstrations began in Tahrir Square, which was the epicenter of the protest movement that ousted Mubarak in February.
The protestors are demanding that the ruling military announce the exact date it plans to hand over power to the newly elected government.
The military has floated a timetable that places the transfer of power late in 2012 or early 2013.
Some protestors are calling for an interim civilian council to take over immediately.
Activists have been holding occasional protests against the military in Tahrir for months, and some have triggered crackdowns by the military or police.
This weekend's violence was the most sustained fighting between the two sides. It began when security forces stormed a sit-in at Tahrir staged by several hundred protesters wounded in clashes during the 18-day uprising in January and February and frustrated by the slow pace of bringing those responsible to justice.
The Associated Press contributed to this story.
