Tuesday's vote was a rematch in districts left undecided in Cairo and seven other provinces in the 9 November first round of the three-round People's Assembly election.
Only 31 seats were decided in last week's vote, with 26 going to the National Democratic Party (NDP), four to the Muslim Brotherhood and one to an independent.
But human rights groups and other monitors reported widespread irregularities, including violence at polling stations, vote-buying and the illegal collective registration of civil servants in areas where they do not live.
The headquarters of the ruling party in the poor Cairo
district of Embaba were attacked and burned late on Tuesday night.
Dozens of men attacked a ruling
party office in Cairo
Witnesses and police said on Wednesday that the attack by a group of 30 to 50 supporters of an independent candidate on the one-storey building took place late on Tuesday, when Egyptian legislative elections turned violent.
"A group of men broke the windows of the building. Then they broke the door down, entered the building and set it on fire," the witnesses said.
"Police have arrested two men in relation to the incident ... The group was made up of supporters of the rival candidate in the elections," a security official said.
The attack took place in the district of Embaba, where NDP candidate Ismail Hilal was running against independent candidate Abdel Moneim Emara.
"Hired thugs are targeting primarily supporters of Muslim Brotherhood candidates," said the Independent Committee on Election Monitoring in a statement issued on Tuesday.
Supporters of the banned Muslim
The Egyptian Organisation for Human Rights said it witnessed "increasing instances of election bribes ... collective voting and in some cases assaults on voters for not supporting NDP candidates".
Independent monitoring organisations reported that polling stations were closed by security forces and employees of state companies threatened with redundancy if they did not vote for the NDP.
Seventeen people were wounded, most of them in the town of Beni Suaif in Upper Egypt, in violence between supporters of rival candidates.
A woman was shot and wounded near a polling station in Old Cairo, a working-class area in the south of the capital, hospital sources said.
Partisans overturned tables and threw them downstairs during voting in a city centre district.
"Observers are reporting a disturbing escalation of violence throughout polling places in Egypt," the Independent Committee for Election Monitoring said in a statement.
It cited four cases of attacks instigated by supporters of the NDP, in Beni Suaif, in Giza near Cairo, in Atfih on the Nile south of Cairo and in Nasr City, a suburb northeast of Cairo.
Police reported a shotgun blast in Cairo and a fight with knives and sticks in the southern city of Assiut that left three people wounded and in hospital by early afternoon.
"Hired thugs are targeting primarily supporters of Muslim Brotherhood candidates"
Independent Committee on Election Monitoring
Gamal Hamad, a spokesman of the Interior Ministry, told reporters as polling stations were closing that intimidation "was limited" and that police stopped a few people who had been planning to assault voters.
After polls closed, several thousand Muslim Brotherhood supporters demonstrated in front of the main counting centre for the district of Nasr City, protesting that security forces were barring candidates' monitors from attending the ballot count.
Earlier, Brotherhood supporters chanting "Islam is the solution" scuffled with NDP supporters outside a polling station in Heliopolis, another Cairo suburb.
Brotherhood leader Mohammed Mahdi Akef urged supporters to try to protect ballot boxes and prevent tampering.
Egypt's main opposition parties are competing, but so far their showing has been minimal.
None of their candidates won seats in the 9 November vote.
Instead, the election is shaping up as a competition mainly between the government and the Muslim Brotherhood, the most powerful opposition movement.
The second round of the elections takes place on 20 November and the third round on 1 December.