Most of the violence was reported in Muslim Brotherhood strongholds in the Nile Delta, north of Cairo.
While police confirmed the six shooting deaths, Interior Ministry officials blamed the violence on supporters of the banned Brotherhood, which has made sweeping gains in the elections, which concluded with Wednesday's run-off.
The deaths raised to eight the number of people killed in political violence since the elections began Nov. 9. Police in Cairo said about 600 people were wounded in election violence Wednesday, and more than 80 people were arrested.
The two deaths occurred in the northern town of Damietta, said Dr. Mohammed Balboula of Damietta Public Hospital. There was no immediate confirmation from the Interior Ministry.
Government supporters armed with knives, bottles and machetes attacked voters lined up trying to get into several stations, sparking clashes with supporters of the Muslim Brotherhood, the government's main rival.
Police also cordoned off polling stations in the southern city of Sohag, frustrating hundreds trying to vote.
Interior Ministry spokesman Ibrahim Hammad said "the election process is going normally," apart from 10 polling stations where he accused Brotherhood "thugs" of causing disturbances.
Hammad said the police are protecting the judges who supervise polling stations "and helping the voters to reach the ballot box."
Egypt's three-stage elections, which began in November, have been plagued by increasing violence as police and government supporters try to put down a strong showing by the outlawed Muslim Brotherhood, which so far has increased its presence in parliament fivefold.
Two other people died and dozens were injured in the earlier rounds. Independent monitors and human rights groups have reported numerous irregularities, including busing of state employees to polling stations, tampering with ballot boxes, blockading of polling stations, and bribing, intimidating and attacking voters.
The United States sharply criticized the violence, including "intimidation and harassment" and abuse of monitors and voters by Egyptian authorities.
"We've seen a number of developments over the past couple weeks during the parliamentary elections that raise serious concerns about the path of political reform in Egypt," State Department spokesman Adam Ereli said Tuesday.
"Clearly, these actions send the wrong signal about Egypt's commitment to democracy and freedom, and we see them as inconsistent with the government of Egypt's professed commitment to increased political openness and dialogue within Egyptian society."
Washington has pressed President Hosni Mubarak, one of its top allies in the region, to bring greater democracy to Egypt, making the country the cornerstone of President Bush's policy of encouraging reform in the Middle East.
But Wednesday's voting — a runoff to the third and final round of the elections — saw a continuation of the violence and police blockades in Brotherhood strongholds.
"What are you afraid of? Why aren't you letting them inside?" Mohammed al-Mursi, the Brotherhood candidate in Zagazig, shouted at police, who sealed off a polling station in the Nasiriyah district, preventing hundreds from voting.
Police blocked the station even before polls opened. When a judge who was supervising polling arrived and protested, the police only let him and a few women enter. A group of about 25 women then pushed through the cordon but were stopped by other police.
"Nobody is entering here," a police officer yelled to the crowd, which continued to push the phalanx of officers. The polling station's doors were closed.
One woman who managed to vote, Umm Mohammed, 45, criticized the police, saying: "The right to vote is the simplest right for any Egyptian."
At another Zagazig station, a battle raged between Brotherhood members and government supporters wielding knives who attacked voters trying to push their way past a police blockade. Police fired tear gas from time to time but did not arrest the government supporters. One would-be voter was bleeding from the head.
The government arrested hundreds of Brotherhood members before Wednesday's vote.
The Brotherhood has 35 candidates in Wednesday's runoff for the remaining 127 of 444 seats in parliament. Polling is taking place in nine provinces where no candidate received more than half the vote in the third round of polling Dec. 1.
So far, Mubarak's ruling National Democratic Party and its allied independents have won 222 seats. The Brotherhood has taken 76 seats, a large jump over the 15 seats it held in the outgoing parliament.
Independents have won two seats and other opposition parties have taken 11.
In the Delta town of Dumyatt, police fired tear gas and rubber bullets at voters during clashes outside at least one polling station, Brotherhood officials said.
In the north Sinai town of el-Arish, clashes broke out between police blocking polling stations and frustrated voters, an Associated Press reporter said.
An Interior Ministry official said at least 30 people had been hurt in clashes in el-Arish and three Nile Delta provinces.
In the southern city of Sohag, police blocked about 400 voters from entering Mohammed Farid School, which was being used as a polling station.
"They say the school is closed. They want to allow only NDP supporters to vote here. I'm very upset. This injustice must stop," said grocer Abdel Moneim, 55.
The head of the General Elections Committee in Sohag, Judge Abou Magd Issa, said he had received no written complaint from voters. Asked why he did not walk to the school, 150 yards from his office, the judge said: "I have people visiting the polling centers and reporting to me. It is up to the security services to maintain security outside the polling stations. I cannot control them."
In the outgoing parliament, the NDP had 398 seats, the Brotherhood had 15, and true independents 23 and opposition legislators had 16.
The Muslim Brotherhood calls for implementing Islamic law but has long been vague about what this means. It campaigns for head scarves for women and against immodest dress, but it insists it stands for a more moderate version of Islam than in Saudi Arabia.