The Egyptian army deployed troops in Cairo's Tahrir Square on Monday and fired shots in the air to disperse remaining pro-democracy protesters.
A few hundred demonstrators were staying put, state television reported, showing army vehicles in the square and people taking down tents and canopies.
Local authorities say they asked demonstrators to allow traffic to move through the square, after local shopkeepers clashed with protesters for interfering with their businesses.
Demonstrators reportedly refused, so the military and riot police moved in.
The protesters responded by throwing stones and rocks at the security forces and several protesters were injured in the clashes, officials said. Activists said several protesters had been arrested.
Members of the April 6th protest movement say the military did not just storm the square, but attacked the mosque where protesters had sought shelter.
Al Jazeera's Sherine Tadros, reporting from Tahrir, said: "There was a split when it came to protesters who wanted to stay and those who wanted to move out.
"There were a good 200 to 300 people who were still camped out earlier. Now it's filled with tanks and army soldiers.
"They've essentially driven out all the people. There do seem to be some civilians moving around but the army is continuing to move out anyone trying to get back into the square."
"People have been telling us, 'They can do what they want but we will just come back once they leave'."
Egyptian protesters had said they would suspend their sit-in at the square during the Muslim fasting month of Ramadan, which began on Monday, but would return to the square to press for reforms after the month was over.
Activists have been occupying Tahrir Square, the epicentre of protests that toppled President Hosni Mubarak, since July 8 to denounce the military rulers' handling of the transition.
The crackdown comes two days before Mubarak goes on trial for his role in killing protesters during the uprising centred on Tahrir Square that drove him from power on February 11.
Twenty-six political parties and protest movements said on Saturday in a joint statement that their three-week sit-in had succeeded in achieving some of their demands, "pushing the Egyptian revolution a step forward".
"But based on our belief that sit-ins are a means, and not a goal, the political parties and youth movements have decided to temporarily suspend their sit-in during the holy month of Ramadan," they said.
The parties stressed that they "will return once again after Eid [feast marking the end of Ramadan] to protest peacefully in Tahrir Square so that the rest of the demands are met".