Saturday's gains by the banned but tolerated Brotherhood came despite cordons of police firing tear gas and rubber bullets in what appeared to be a determined government effort to block opposition voters and stop the Islamic-based organisation from building momentum.
Early Interior Ministry figures showed the Brotherhood increasing its share in parliament to at least 72 seats, a more than fourfold jump over its representation in the outgoing parliament.
A a third and final stage of voting is scheduled on 1 December, with a runoff likely six days after that.
The outcome, if it becomes final, would push the Brotherhood theoretically past the number of seats needed under new constitutional rules to nominate a presidential candidate in 2011.
Armed backers of Islamist and secular politicians engaged in fierce clashes that - combined with police action - severely curbed turnout and scarred an election that was seen as a test of Egypt's pledge to open its authoritarian political system.
Non-government organisations and judges monitoring the polls complained that security forces blocked thousands of the 10 million eligible voters from entering polling stations in nine provinces where 122 seats were in play after no candidate garnered more than half the vote in the second round of polling six days ago.
Before Saturday's vote the Brotherhood - Egypt's largest Islamist group - had racked up 47 of 186 decided seats. President Hosni Mubarak's NDP had won 122 seats and 17 went to other candidates in voting that began on 9 November.
Mubarak cancelled his visit to a
EU-sponsored summit in Spain
While there was no chance that the Brotherhood would unseat the NDP, which with its allies held 388 of 454 seats in the previous People's Assembly or parliament, the Brotherhood showing was a stunning outcome for an organisation that previously held only 15 seats, with 41 occupied by other parties. Mubarak appointees fill 10 seats.
The president, meanwhile, unexpectedly cancelled plans to attend a EU-sponsored summit on Sunday in Barcelona, Spain, at which Europe was to push for increased ties by linking billions of euros in economic aid to sweeping democratic and other reforms on the Mediterranean's southern and eastern rims.
Sulayman Awwad, the presidential spokesman, said the press of developments in the Arab world were behind the cancellation and denied that election violence was the cause.
Judge Hisham al-Bastawisy, deputy head of Egypt's Court of Cassation, denounced the violence in an interview with the Arab satellite television channel Al-Arabiya.
"What we've been hearing since early morning about what is happening at polling stations indicates this it is not an election. It's a battle. Judges have been attacked, some wounded, some prevented from entering polling stations," al-Bastawisy said.
Ali Abd al-Fattah, a senior Muslim Brotherhood member, said police arrested 680 members and supporters nationwide on Saturday, nearly 120 of them in Alexandria alone.
"What we've been hearing since early morning about what is happening at polling stations indicates this it is not an election. It's a battle"
Judge Hisham al-Bastawisy
The first stage of voting was mainly peaceful, but - after an initially strong showing by the Brotherhood - violence and police interference increased greatly.
The Muslim Brotherhood was banned in 1954 and later that year accused of trying to assassinate Gamal Abdel Nasser, the interior minister who became president in 1956.
It renounced violence in the 1970s and gets around the ban on its activities by fielding candidates as nominal independents whose Islamic-based positions and sympathies are well known to voters.