On Saturday, thousands of riot police were deployed in constituencies where the Brotherhood had candidates, in many cases sealing off polling stations or limiting the number of people who could go in, witnesses said.
A leading judge said some judges had left in protest against the police action and taken the ballot boxes with them.
"Security forces besieged some of the polling stations, blocking some voters from entering and allowing others in," said judge Ahmed Mekki, who is in charge of an informal election monitoring effort by the judiciary.
Another judge, the deputy chief of the court of cassation who is also member of the election monitoring committee, told Aljazeera the voting was cancelled in some constituencies but declined to say how many.
"When the judges objected to the police preventing of voters from entering polling stations, they were insulted by the police," Judge Hisham Bastawisy said.
"After that, some judges in these polling stations called for suspension of voting," he said.
Brotherhood supporters protest
at an Alexandria voting station
Voter Taher Abdel Fattah said he had gone to cast his vote in the port city of Alexandria but could not do so because of the police cordon around the polling station.
"The government told us we should vote and decide the future of this country. Now the same government is stopping us from voting.
"This is disgusting. There is no freedom here," he said.
"Tomorrow they will say the election was fair and everyone is happy. It will all be lies. We are ruled by liars and thugs," said Mohamed Ibrahim, 31, who was trying to vote, too.
In the late afternoon in the Nile Delta city of Tanta, a line of riot police, three men deep, prevented people from voting.
"Tomorrow they will say the election was fair and everyone is happy. It will all be lies. We are ruled by liars and thugs"
When a Reuters correspondent tried to take a photograph, police manhandled him, briefly detained him and took away the memory card of his camera.
In Quz constituency, two polling centres were closed, a Muslim Brotherhood candidate there told Aljazeera. Security forces were filmed surrounding the centres.
A judge said that 10 voters had cast ballots and that he told the head of the election committee that the low turnout was due to police interference.
Scattered violence marred the fourth day of voting in Egypt's long electoral process, which ends on 7 December.
More than 20 people were injured when voters and police clashed at a polling station in Alexandria's Dakhaila constituency. Police fired tear gas to disperser voters who had tried to pass through security at the voting centre.
A police officer stands guard as
women wait at a polling station
Independent monitors said members of both the ruling National Democratic Party (NDP) and the Brotherhood took part in Saturday's brawls.
Machetes and clubs
The elections on Saturday were especially heated after the Brotherhood, which fields candidates as independents because the government refuses to recognise it, won more seats than President Hosni Mubarak's NDP in voting last Sunday.
The Brotherhood said police had detained 628 of its supporters in seven provinces since the early hours.
The Interior Ministry said police fired tear gas and detained 78 "troublemakers", including Islamists in Tanta after they threw stones at police. Security sources said the number of detainees had reached 159.
In the Nile Delta village of Hayatim, men with machetes and clubs attacked Brotherhood organisers outside polling stations, witnesses and election monitors said.
This man managed to cast his
vote in Kaliob, north of Cairo
The Independent Committee on Election Monitoring (ICEM) said NDP "thugs" were intimidating observers and people who looked like they might be Brotherhood sympathisers.
Another group, the Arab Centre for the Independence of the Judiciary, said that in the Nile Delta town of Benha, Muslim Brothers threw stones, hit voters and damaged vehicles. Police intervened and closed down some polling stations, it said.
The Brotherhood now has 47 of the 444 elected seats in parliament, against about 120 for the ruling party.
The Brotherhood, which advocates political freedoms and wants to bring Egyptian law closer to Islamic law, is contesting 41 of the 121 seats at stake on Saturday, mostly in direct competition with the NDP.