At least one person was killed in the Mediterranean port city of Alexandria on Sunday, and police used tear gas to break up rioting in the Nile delta.
Scores of voters and campaign workers were reported injured, some hurt by knives, chains and Molotov cocktails, in clashes across the nine provinces where 1706 candidates were vying in 72 constituencies.
The National Democratic Party (NDP), the party of President Hosni Mubarak, held an 80% majority heading into the three-stage vote, which concludes on 1 December.
But the Muslim Brotherhood did unexpectedly well in the first round last week, raising tensions higher.
Ibrahim Hammad, a spokesman for the Interior Ministry, accused the organisation of using thugs to intimidate voters and attack other candidates' supporters.
Driver Mohammed Khalil Ibrahim
was killed in Alexandria's clashes
"I say with all sorrow that most of the [thugs] are used by candidates of the religious current [the Brotherhood]," Hammad said.
But Gamal Hishmat, a Brotherhood candidate in the Nile delta town of Damanhur where rioting was widespread, said the ruling party and police were responsible.
"We are facing a corrupt oppressive government and an unarmed people confronting it with stones. We are witnessing an uprising in Damanhur," he said.
The Muslim Brotherhood, in a statement after polls closed, said 306 people, including two women, were arrested in the nine provinces.
Killed by thugs
The Egyptian Organisation for Human Rights and police said the dead man caught up in clashes in Alexandria, was a driver for an independent candidate and identified him as Muhammad Khalil Ibrahim.
Ibrahim was beaten to death by a group of thugs hired by the party's official candidate, said Muhammad Zarai, head of the National Campaign for Monitoring Elections.
The Interior Ministry denies Saif
al-Din al-Qabari was stabbed
In a separate incident, Aljazeera reported the NDP's dissident candidate in Alexandria, Saif al-Din al-Qabari, was stabbed.
Egypt's Interior Ministry denied the claim, saying he was slightly injured when trying to pull a knife from the hand of a rioter.
In Damanhur, 140km north of Cairo, riots started outside 10 polling stations, a police official said. Knives and steel chains were used by Muslim Brotherhood supporters, the official said, and at least 20 supporters of the organisation were taken into custody.
Sameh Bakr, a Muslim Brotherhood campaign worker, said police sealed off a number of polling stations, firing tear gas and bullets to keep voters away.
The Egyptian Organisation for Human Rights said three men stabbed one campaign worker for a Muslim Brotherhood candidate in the neck inside a polling station near Damanhur.
He was transferred to a hospital and was in a critical condition.
Muslim Brotherhood supporters
in Alexandria chanting slogans
At another polling station, Muslim Brotherhood supporters attacked two buses and threw kerosene bottles at the car of a campaign worker, damaging it, police said.
In the Suez Canal city of Ismailia, witnesses said a Muslim Brotherhood candidate's brother was shot and wounded by the cousin of the NDP candidate at one polling station.
Sunday's violence was in contrast to the first round of voting on 9 November which passed in relative peace and saw the banned Brotherhood double its representation in parliament in that round alone.
Egyptian Organisation for Human Rights said one of its monitors was kidnapped in Port Said, another Suez Canal city, and said candidates' representatives were being denied access to polling stations.