Khaled Desouki / AFP - Getty Images

Egyptian demonstrators confront riot police during protests outside the defense ministry in Cairo's Abbassiya district on May 4, 2012.

Protesters threw rocks at troops guarding Egypt's defense ministry on Friday as thousands marched in Cairo to denounce violence against demonstrators and the exclusion of candidates from the presidential election.

The crowd hurled projectiles and insults at the soldiers sent to defend the ministry after 11 people were killed in clashes there on Wednesday, and called for the overthrow of the head of the ruling army council, Field Marshal Hussein Tantawi.

The army fired back with water cannons then teargas and riot police surged towards the crowd with batons. Scores of wounded protesters were taken away on motorcycles and dozens of soldiers were injured.

"O Tantawi, good morning, this is your last day," shouted the crowd, and "field marshal leave, the people are dangerous."

The street violence comes less than three weeks before an election that represents the first chance for Egyptians to freely choose their leader. A successful vote would mark the most important step in a messy transition to democracy since the overthrow of autocratic leader Hosni Mubarak 15 months ago.

Last-minute changes to the line-up of contenders, bickering over a new constitution and suspicion that the military will continue wielding power after a new president is chosen are making for a chaotic backdrop to the campaign.

In Egypt, chaos is pinned on military's incompetence

The troops pressed forward when protesters began cutting through barbed wire used to seal off the ministry building in Cairo's central Abbasiya district.

Protesters ripped down a metal fence at an underground railway construction site to build a barricade. Some cried "God is greatest" as army helicopters swooped overhead.

The teargas scattered the crowd hundreds of meters down the rock-strewn streets where they regrouped. Troops blocked off a street to the ministry using armored personnel carriers and some fired shots in the air.

PhotoBlog: Thousands protest in Cairo as military fires back with tear gas and water cannons

"The crowd is coming here with sharp weapons. We have batons and water cannon and teargas to disperse them," said one commander. "Some of them believe if they kill a soldier they will go to heaven. What do you expect us to do?"

The Health Ministry said 59 people were injured, most of them from inhaling teargas, and five were taken to hospital.

As dusk approached, gunfire could be heard close to a mosque in the center of the capital.

Election disputes
Tension surrounding the election rose a notch on Wednesday when unidentified assailants fired at protesters camping near the defense ministry, starting clashes that the security forces seemed unable or unwilling to quell.

Many of those protesters were hardline Salafi Islamists upset that their candidate was ruled out of the vote, which begins on May 23 and 24 with a run-off in June.

The Muslim Brotherhood, which dominates parliament, saw its first choice disqualified too, handing a potential advantage to Mubarak-era contenders such as former foreign minister Amr Moussa and ex-prime minister Ahmed Shafiq.

Some Egyptians see the last-minute changes to the candidate line-up as proof the generals are trying to manipulate the vote.

"Remnants of Mubarak's regime are not eligible to assume any power," Hashem Islam, a sheikh from Egypt's highest authority of Sunni Islam, Al-Azhar, told protesters at the defense ministry.

Several thousand Islamists, liberals and left-wing revolutionaries also massed in Tahrir Square, headquarters of the street movement that has transformed decades of tightly-controlled Egyptian politics.

Banners draped in Tahrir demanded implementation of a law banning figures from the Mubarak era from high office. Shafiq was briefly disqualified as a result of the law, but still found his way back into the final line-up of presidential candidates.

Members of the ruling military council on Thursday renewed a pledge to exit politics after handing power to the new president by mid-year. They said the handover could come earlier in the unlikely event that one candidate wins outright in the first round.

But tension between the army's interim government and the Islamist-dominated parliament has left Egypt in a state of policy paralysis that is deepening an economic crisis caused by more than a year of political turmoil.

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