Deadly clashes sparked by army move to shut down sit-in outside cabinet offices, as election process continues.

Al Jazeera’s Rawya Rageh was on the ground in Cairo when protesters were being attacked by the military [Al Jazeera]

At least two people have been killed and more than 220 others injured in Egypt after soldiers stormed an anti-government protest camp in Cairo, prompting a series of violent clashes, witnesses and state television reported.

Protesters set cars alight and threw stones at military police in the Egyptian capital, after a wounded activist said he had been arrested and beaten by soldiers at a sit-in near the parliamentary building earlier.

Clashes began at dawn on Friday, as soldiers fired shots in the air in order to try and disperse around 300 demonstrators, who had been angered by video that appeared to show the activist badly beaten after his arrest.

The initial confrontation sparked ongoing clashes that resulted in security forces storming the protest camp outside the Egyptian cabinet building. Violence has centred on al-Kasr al-Aini street, adjacent to Tahrir Square, on which many government buildings are located.

“The confrontation between the protesters and the military … is clearly taking a turn for the worse,” reported Al Jazeera’s Rawya Rageh from Cairo.

“Very ugly scenes witnessed here throughout the day, including scenes of men in uniform perched on the rooftops of buildings, throwing whatever they can lay their hands on on protesters, including sheets of glass, bottles, rocks and at one point even furniture.

“Very unpleasant scenes, including some of these soldiers gesturing obscenely towards the protesters, and one of them even at one point urinating on the protesters gathered below,” she said.

The state news agency reported that 32 security forces personnel were among the wounded.

The country’s ruling military council issued a statement blaming the violence on the protesters, saying that the clashes were part of a conspiracy to derail the country’s elections process, which is ongoing.

It said it would continue to act firmly against any attempts to overrun government buildings, and that its soldiers did not move to disrupt the sit-in.

It denied that tear gas or live ammunition had been used, and said the issue would be transferred to the Egyptian prosecutor’s office to be investigated.

Activist reportedly beaten

The clashes, which had raged since dawn, started after a bloodied protester said he had been arrested by soldiers and beaten up, infuriating his comrades, who began throwing stones at the soldiers, witnesses said.

The troops responded by firing shots in the air and using water cannons, before throwing stones back at the protesters from the roof of the nearby parliament building.

The activist, identified by other protesters as Abboudi Ibrahim, was arrested as he left the sit-in outside the cabinet office in central Cairo.

Protesters have been occupying the area in front of the cabinet office for more than two weeks, preventing Prime Minister Kamal Ganzouri and his cabinet from meeting there. They are demanding that the country’s Supreme Council of the Armed Forces (SCAF) immediately cede authority to a civilian government.

Video of Ibrahim showed his eyes bruised and swollen, his head wrapped in gauze and blood dripping from his nose.

“It’s a very intense scene … the smoke billowing from the fire at [the transport ministry],” reported Al Jazeera’s Rageh from the scene of the clashes. “People are incredibly angry that they are being attacked by their own military.”

Tensions high

“Tensions between the people and security officers is so inflamed that anything that happens just blows up. There is no trust between the two sides,” said Hussein Hammouda, an activist who resigned from the police in 2005 to protest police practices.

“Doctors [and] first aid responders are telling us that dozens of people who are injured are afraid to actually get in ambulances and be transferred to hospitals, in fear of being detained by security forces,” reported Rageh.

Reports indicated that several people had been taken into military custody, but were released soon after.

Al Jazeera’s Evan Hill, an online producer, was beaten and briefly detained by police during the clashes. Police confiscated his personal belongings, including his phone and passport.

Council members resign

Moez Abdel Fattah and Ahmed Khairy, members of the newly formed advisory council set up by SCAF, have resigned in protest against the violence today.

The council itself has met in the capital to discuss the situation, with reports indicating that several other members are also considering resigning.

The military, in charge since president Hosni Mubarak’s overthrow in February, has said it will step down once a president is elected by the end of June next year.

The clashes on Friday come as Egypt ended its second round of voting in a long and complicated election process that began on November 28. Voting took place in parts of greater Cairo, Ismailiya and Suez in the east, Aswan in the south and in the Nile Delta regions in the north.

The Muslim Brotherhood’s Freedom and Justice Party and Salafi al-Nour party, both Islamist groups, have so far won the most seats, with a coalition of liberal parties lagging behind.

Results from the latest round of voting, which concluded on Thursday, are due in the coming days.