On Wednesday, live footage from Cairo showed smoke engulfing Nahda square and there were reports of tear gas and birdshot being used on supporters of deposed president Mohamed Morsi, who was removed from power on July 3, Aljazeera reported.
"Many people are being killed right now ...What we can expect is only worse," said Laila, a member of Egypt's Anti-Coup Alliance, a pro-Morsi group. "What's happening now is a crime against humanity."
Reuters said at least 15 people were killed. Laila said the figure was at least 16.
"I see a lot of black smoke and helicopters circling," said Al Jazeera's Dorothy Parvaz, reporting from Cairo.
State media confirmed that security forces had started implementing their phased plan to disperse the protesters.
The action follows weeks of warnings from the interim leadership that force would possibly be used to clear the protesters.
At least one person was killed on Tuesday, and many others injured in clashes between supporters and opponents of Egypt's ousted president.