Riot police blocked entry to polling stations in some Muslim Brotherhood and opposition strongholds in elections that are being seen as a potential watershed for Egypt after the technically-banned Brotherhood made gains in previous rounds.
The respected judges' syndicate responsible for supervising the elections has mounted an unprecedented challenge against the state.
It has secured more guarantees of transparency and publicly denounced irregularities in the previous rounds, threatening a mass walkout if police continued to obstruct the process.
A spokesman for the judges, Mahmoud al-Houderi, threatened to pull the judges out if the government prevents people from voting.
"We have witnessed in [some constituencies] the sealing off polling stations to voters by police... Judges monitoring the stations have been prevented from opening them to let in voters," Mr Houderi told the BBC.
In the Nile Delta village of Bossad, voters of all ages and sexes could be seen climbing over walls with rickety wooden ladders to enter polling stations whose main entrances were blocked off by phalanxes of riot police.
Fires ignited by tear-gas grenades that landed on thatched roofs burned down three houses in the same village, near the city of Mansura.
The same confusion and anger prevailed in Al-Adwa, a village near the city of Zagazig where the head of the Brotherhood's parliamentary group, Mohammed Morsi, was contesting a seat.
Brotherhood gains
More than 10 million Egyptians were eligible to vote in Thursday's third and final round, with 136 of the parliament's 454 seats up for grabs.
The Muslim Brotherhood has seen a 20 percent increase in the number of its representatives in the Egyptian parliament following the two previous rounds of voting, taking it to 76.
The banned party gets round the restrictions on its activities by fielding candidates as independents.
About 500 members of the Brotherhood were arrested ahead of the vote in the governorates where Thursday's election would be fought out.
The Islamist movement said most of those rounded up were campaign organisers in the various constituencies.
They included Daqahliya, Kafr al-Sheikh, Sharqiya, all in the Nile Delta, and Suhaj in the south.
It accused the ruling National Democratic Party (NDP) of President Hosni Mubarak of wanting to thwart its election campaign.
The ruling NDP has suffered a number of setbacks, but has won 201 seats so far and is still expected to win the majority of seats.
The final results will not be known for another week.
The Muslim Brotherhood's unprecedented success has altered the balance of power between the government and the opposition.
It has given the Brotherhood a legal platform under parliamentary immunity rules to challenge and question the ruling NDP's policies without fearing the usual arrests and harassment.
Campaign slogan
Campaigning under the slogan "Islam is the solution", the movement founded in 1928 made major gains in the first two phases of the election, winning 76 seats, already five times their tally in the outgoing parliament.
With a success rate hovering around 70 percent, the Brotherhood could reasonably hope to reach the symbolic 100 mark as it was fielding a total of 49 candidates in the 68 constituencies taking part in the voting.
Although its dominance of the People's Assembly was not at risk, President Hosni Mubarak's NDP will have to secure close to 100 more seats in order to retain the two-thirds majority required to change the constitution and pass emergency laws.
The violations reported by opposition parties, journalists and independent monitors in last week's second phase runoffs prompted expressions of concern from the regime's US ally.
"The Egyptian government has a responsibility to provide an atmosphere for its people in which they can feel as though they are not encumbered, they are not barred from or under the threat of violence or coercion," the State Department said.