Sustained bursts of automatic weapons fire and powerful single shots rattled into the square starting at around 4 a.m. Thursday, and continued for more than an hour later.
Protest organizer Mustafa el-Naggar said he saw the bodies of three dead protesters being carried toward an ambulance. He said the gunfire came from at least three locations off in the distance and that the Egyptian military, which has ringed the square with tank squads for days to try to keep some order, did not intervene.
Pro- and anti-government supporters were clashing in Egypt's capital Wednesday morning.
Throughout Wednesday, Mubarak supporters charged into the square on horses and camels brandishing whips while others rained firebombs from rooftops in what appeared to be an orchestrated assault against protesters trying to topple Egypt's leader of 30 years. Three people died in that earlier violence and 600 were injured.
The Associated Press reported that some people were injured when protesters on the two sides began hitting each other with sticks in Tahrir Square Wednesday night. That's where demonstrators against Egyptian President Hosni Mubarak have been protesting for days.
In multiple incidents, journalists covering Egypt's unrest were pummeled, hit with pepper spray, shouted at and threatened by loyalists to President Hosni Mubarak as the scene at anti-government demonstrations suddenly turned ugly.
The Committee to Protect Journalists described a series of deliberate attacks. The New York-based CPJ called on the Egyptian military to provide protection for reporters.
Al Jazeera kept its camera crews away from the square and instead relied on reporters of Arab descent who had flip cameras and tried to do their work by blending in with the crowd, said Al Anstey, the network's managing director.
Mubarak announced that he will not run for re-election and that he will spend the rest of his term focusing on the peaceful transfer of power.
Thousands of were still on the streets Wednesday, even though the military called for an end to the demonstrations.
Pro-Mubarak demonstrators have been rallying support for him in Cairo. Some fear shortages of food and other necessities will continue if the protests don't end.
President Barack Obama said an orderly transition must begin now.
"The process must include a broad spectrum of Egyptian voices and opposition parties. It should lead to elections that are free and fair," Obama said on Tuesday.
The Associated Press contributed to this report.