At least three people were killed and 257 wounded in Cairo on Friday as troops fought demonstrators in the worst violence since Egypt began its first free election in six decades.

In a pattern that has recurred during nine months of army rule since President Hosni Mubarak's overthrow in February, the confrontation swiftly grew as more people took to the streets.

The Health Ministry said three people had been killed and 257 wounded in the unrest in the city centre. A third died from gunshot wounds, a worker at a makeshift field hospital said.

Egypt's Dar al-Iftah, the body responsible for issuing fatwas (religious recommendations) said one of its top officials, Emad Effat, was killed during the violence, the state news agency MENA said.

Clashes raged on after nightfall, with protesters throwing petrol bombs and stones at the cabinet building, breaking windows and security cameras. Soldiers fired at demonstrators hurling rocks at the parliament building. It was not clear if they were using rubber bullets or live ammunition.

The violence erupted the previous night when military police tried to break up a sit-in in front of the cabinet offices, activists said. That ignited clashes that quickly turned the streets around parliament into a rock-strewn battle zone.

The ruling military council, in a statement read on state television, denied troops had tried to disperse the sit-in.

It also denied troops had used fire-arms and said the violence started when one of the officers maintaining security outside parliament was attacked while on duty. The public prosecutor would investigate that incident, the council said.

A new civilian advisory council that was set up to offer guidance to the army generals on policy said it would resign if its recommendations on how to solve the crisis were not heeded.

Presidential candidate Amr Moussa, who is a member of the civilian council, told an Egyptian satellite television station, the council had suspended its meetings until the military council meets its demands that include an end to all violence against demonstrators.

By early afternoon, ambulance sirens were wailing as troops tried to disperse around 10,000 protesters with truncheons and what witnesses said appeared to be electric cattle prods.

Reports of beatings of well-known pro-democracy activists buzzed across social media and politicians from Islamists to liberals lined up to condemn the army's tactics.

Even if the sit-in was not legal, should it be dispersed with such brutality and barbarity? asked Mohamed ElBaradei, a presidential candidate and former U.N. nuclear watchdog head.

The sit-in outside the cabinet office was a remnant of far bigger protests last month around Cairo's Tahrir Square in which 42 people were killed shortly before voting began in Egypt's first election since a military council took over from Mubarak.

The council wants to spoil the elections. They don't want a parliament that has popular legitimacy unlike them and would challenge their authority, said Shadi Fawzy, a pro-democracy activist. I don't believe they will hand over power in June.

In Friday's disturbances, cars were set alight and part of a state building was torched.

Troops and unidentified men in plain clothes hurled rocks from the roof of one parliament building onto protesters who were throwing stones, shards of glass and petrol bombs.

Demonstrators burned piles of car tyres to send up plumes of black smoke and block the view of the street from above.

The head of the military council, Field Marshal Mohamed Hussein Tantawi, ordered that everyone wounded in the fighting be treated in army hospitals, state television said.

An army source said 32 security personnel had been wounded while trying to stop protesters from breaking into parliament.

Ziad el-Elaimy, a leading figure in the liberal Egyptian Bloc, who ran for parliament in Cairo, said he was beaten by security forces when he arrived to witness the scene.

When he protested, army officers told him: To hell with you and your parliament, according to Elaimy.

BATTLEGROUND

The actual voting in the election, which is staggered over six weeks, has been mostly peaceful since it began on November 28.

A big first-round turnout had partially deflated the street protests against army rule, which prompted the government to resign and the generals to pledge to step aside by July.

On Sunday, a new cabinet is to hold its first full meeting since it was sworn in on December 7 and plans to weigh new austerity measures to address a wider-than-expected budget deficit.

Protesters have occupied an area outside the cabinet office since late November, forcing the government to meet elsewhere.

They said the army provoked the violence, which worsened after images appeared online of an activist, named as Abboudi Ibrahim, being supported by a crowd, his face badly bruised and eyes swollen and shut after he was detained by military police.

Protester Bebars Mohamed, 19, said he was at the sit-in when military police grabbed Ibrahim.

The army pushed us away from Parliament Street and burnt the tents. They threw rocks and glass on us, he said.

ISLAMISTS LEAD IN ELECTION

The clashes broke out after two days of voting in the second round of the election on Wednesday and Thursday. Turnout again appeared high as voting moved to districts of greater Cairo, Suez, Ismailiya, Aswan and parts of the Nile Delta.

The Muslim Brotherhood's Freedom and Justice Party (FJP) said it expected to keep its first-round lead but that it was not clear whether its vote share would stay around 40 percent.

Early indications showed the FJP still in the lead, followed again by the hardline Islamist Salafi al-Nour party, with the liberal Egyptian Bloc in third place, state newspapers said.

The army is in charge until a presidential election in mid-2012, but parliament will have a popular mandate that the military will find hard to ignore as it oversees the transition.

Prime Minister Kamal al-Ganzouri, who has made law and order a priority for his new interim government, has said little.

The prime minister said he now had presidential powers, but he hasn't moved or spoken or issued clear directions, said Adel Soliman, head of Cairo's International Centre for Future and Strategic Studies. There is complete silence from all those in power.

(Additional reporting by Marwa Awad, Omar Fahmy, Shaimaa Fayed, Ahmed Tolba, Ashraf Fahim, Amr Dalsh; Writing by Tom Pfeiffer; Editing by Alistair Lyon)