Deadly clashes pitting troops and police against protesters rocked Cairo's political centre for a third straight day on Sunday, overshadowing the count in the first post-revolution vote which shows Islamists in the lead.
At least 10 people were killed in the violence that also destroyed a historic library housing priceless archives.
The violence marred the count in the second round of a multi-stage election which saw a 67 percent turnout and in which the largest Islamist parties claimed victory.
The Muslim Brotherhood's Freedom and Justice party (FJP) said it won 39 percent of votes in the party lists, while the Al-Nur party, which represents the more hardline brand of Salafi Islam, claimed more than 30 percent of votes in the lists.
The ruling military, which took power when Hosni Mubarak was ousted in February, has decided on a complex election system in which voters cast ballots for party lists, which will comprise two thirds of the lower house of parliament, and for individual candidates for the remaining third.
"The FJP is definitely number one, we have come second," Al-Nur spokesman Mohammed Nur told AFP.
In central Cairo, armed forces detained over 180 people including minors, the prosecutor's office said, as street battles raged outside parliament and government offices where protesters are demanding an end to military rule.
The clashes were the deadliest in weeks and have sparked a furious debate over the army's role during the transition.
Some argue that the protesters are sabotaging the elections, while others say the army is stalling in ceding power to a civilian authority.
Much remains unclear about how the new parliament will function and how much power it will be given by the Supreme Council of Armed Forces (SCAF), headed by Mubarak’s former defence minister Field Marshal Hussein Tantawi.
Demonstrators hurled stones and pieces of metal over a concrete wall erected by troops on a wide avenue leading from Tahrir Square to the seat of government, AFP journalists reported.
By afternoon, troops retreated and riot police faced off with the protesters, who used metal sheets as barricades.
Men in civilian clothes on the roof of a building threw stones at protesters, who shot fireworks back.
Outrage flared as furious protesters brandished the front page of a local paper showing military police clubbing a veiled woman after having ripped her clothes to reveal her bra.
In the picture and YouTube footage of the incident, the woman is sprawled on the ground, helmeted troops towering over her. One is seen kicking her, and later she appears unconscious, her stomach bared and her bra showing.
Other pictures circulating on social media networks that have enraged protesters include one of a military policeman looming over a sobbing elderly woman with his truncheon.
More footage showed army troops beating two protesters, a man and woman, before leaving their motionless bodies on the ground.
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The health ministry said late Saturday that 10 people had been killed and at least 500 wounded since Friday.
The clashes also left the Institute of Egypt in flames.
The centre for the advancement of scientific research was founded in 1798 during Napoleon Bonaparte's expedition to Egypt, and contained more than 200,000 precious documents and manuscripts.
On Sunday, a group entered the premises to recover manuscripts, some of which were burned, AFP correspondents said.
"We are trying to save whatever we can of these historic documents. The building can collapse any minute," said Olfa, clutching a bag of partly burned papers.
Culture Minister Shaker Abdel Hamid called the fire "a catastrophe for science."
"The building contained important manuscripts and rare books which have no parallel in the world," he said on state television late on Saturday.
The authorities have blamed the protesters for the deadly unrest.
The military council late on Saturday posted footage on its Facebook page and on YouTube of protesters ransacking a government office on Friday.
"Is it not our right to protect the people's property?" said a brief message.
Prime Minister Kamal al-Ganzuri raised tensions on Saturday by accusing the protesters of being counter-revolutionaries and denying security forces had opened fire on them.
"Those who are in Tahrir Square are not the youth of the revolution," he told reporters.
"This is not a revolution, but a counter-revolution," added Ganzuri, who also served as premier under Mubarak.
His appointment last month by the SCAF had prompted protesters to launch a sit-in outside the cabinet offices.
The demonstrators want the SCAF to hand over full powers to a civilian administration.
The military has said it will step down only once a president has been elected by the end of June in the final stage of a protracted transition.
The clashes pushed stocks down 3.46 percent on Sunday, with the main EGX-30 index plummeting to 3,782.74 points, the lowest since Mubarak was toppled.
More than 40 people were killed in similar clashes between protesters and security forces just before the election's first round in November.