Cairo (CNN) — Clashes broke out in parts of Cairo on Friday as protests against the country’s military government turned violent.

Video from the scene showed some protesters throwing rocks at security forces, and the security forces spraying water cannons at the demonstrators, who were protesting near the country’s Defense Ministry.

At least 59 people have been injured in the clashes in the Abaseya area, and 29 have been hospitalized, Ministry of Health spokesman Khaled El Khatib said.

Egypt’s state-run Nile TV showed at least two members of the military police suffering injuries and being carried away from the front line of the clashes.

Thousands of people descended on downtown Cairo on Friday after several parties urged supporters to voice their outrage about deadly clashes this week and demand the resignation of Egypt’s interim military government.

At least 11 people were killed and scores injured Wednesday in violence in Abaseya, where a sit-in protest has been going on for a week outside Egypt’s Defense Ministry.

As the latest clashes gathered steam, Nader Abdel Aziz, a human rights lawyer, reported seeing warning shots fired in the air by security forces, as well as military helicopters hovering over the scene.

Some military officers have been injured by rocks thrown by protesters, he said.

Alaa Al Iraqi, a spokesman for Egypt’s Supreme Council of the Armed Forces, said officials warned protesters that the Defense Ministry was “a red line” that shouldn’t be crossed.

“They threw rocks first at the military police soldiers, insulted them and pushed through barbed wire,” the spokesman said. The rock-throwing injured several soldiers.

“No live ammunition of any kind was used except for standard protocol for dealing with riots,” he said.

The protests came against a backdrop of frustration about the pace of reform since Hosni Mubarak was ousted as president last year and amid concern that Egypt’s military leadership is delaying the transition to civilian rule.

The Muslim Brotherhood’s political wing, the Freedom and Justice Party, was among those taking part in another protest in Tahrir Square, the heart of Egypt’s protest movement, under the banner of “stopping the bloodshed.”

At least three stages had been set up in the square, where a mostly Islamist crowd planned to demonstrate, according to Nile TV. Many are supporters of Islamist candidate Hazem Abu Ismael, who is among a number of candidates disqualified from the May 23 presidential election.

Ahmed Maher, founder of the liberal April 6 movement, which was among those to join the protests in Abaseya, said it was urging its supporters to pull back.

“We are withdrawing from Abaseya to avoid and limit bloodshed. Some of our field medics will remain behind to assist only,” he said.

The April 6 movement wants accountability from the Supreme Council for the Armed Forces for the deaths of protesters in the Abaseya clashes Wednesday.

The Ministry of Health earlier dispatched 70 ambulances to the Abaseya protests, dubbed the “Final Friday” march. And the Arab Doctors Association set up two makeshift clinics.

The Al Nour Salafi party has boycotted the Abaseya protest.

Egypt’s Supreme Council of the Armed Forces said on its Facebook page Thursday that the clashes in Abaseya were aimed at delaying the presidential elections and stalling the formation of a constituent assembly.

The Supreme Council also said that certain “unnamed” groups have used verses from the Quran calling for jihad, or holy war, to try to draw the military into an armed conflict.

The military had tried to persuade the protesters to move from their position near the Ministry of Defense to Tahrir Square, but they refused, the Facebook statement said.

Controversy about the approaching presidential elections has been growing.

The Muslim Brotherhood’s preferred candidate, Khairat El Shater, who was disqualified from running last month, was referred to the country’s general prosecutor Friday for insulting the election commission.

Abu Ismael was also referred to the general prosecutor for alleged forgery. He was disqualified from standing because of evidence that his late mother had U.S. citizenship, an assertion he has denied.

On Thursday, three other presidential candidates also were referred for alleged violations of election campaign law.

The three candidates — leading independent Abdel Monein Aboul Fettouh; Mohamed Mursi of the Islamist Freedom and Justice Party; and Amre Moussa — were accused of breaking the law by holding meetings on college campuses.

“These infringements by the presidential candidates will be taken very seriously, and they will be questioned as soon as possible. They could be fined,” Adel Saeed, the official spokesman for the general prosecutor, told CNN on Thursday.

The election commission has disqualified about 10 of the 23 presidential contenders, its chief has said. The disqualifications have prompted widespread anger.

International powers have urged all sides to exercise restraint after the clashes Wednesday.

Assailants targeted the protesters in Cairo early Wednesday, medical sources said. At least 150 people were injured, Dr. Ahmed Thabet, a physician working in a field hospital near where the clashes took place, said Thursday.

It was unclear who the attackers were, but they were not wearing uniforms, witnesses said.

The Freedom and Justice Party, the political arm of the Muslim Brotherhood, blamed the Supreme Council for the deaths and injuries in the Abaseya clashes, and it said that the council, not the protesters, wants to delay the transition of power.

A government official earlier denied reports that the military was involved in Wednesday’s violence.

“There were no riot police or military that tried to evict the sit-in by force,” said Gen. Marwan Mustapha, a spokesman for the Interior Ministry.

“We are not sure of the identities of the thugs that attacked the peaceful protesters. The military only protects the vicinity of the ministry and blocked some roads leading to it.”

Clashes have erupted in Egypt since an uprising led to the toppling of Mubarak in February of last year, with protesters demanding the military leaders who took over hand over power to a civilian administration.