Nine governorates were due to vote in 127 runoffs on Wednesday in the third and final phase of the elections amid growing domestic and international criticism over the conduct of the polls.
The officially banned Muslim Brotherhood made spectacular gains in the first two phases of polling, already securing 76 seats in the future People's Assembly, nearly five times their 2000 tally.
According to independent monitoring groups and opposition parties, security forces started blocking off polling stations early in the day.
Previous rounds of voting were marred by voter obstruction in some constituencies, with security forces sometimes clashing with frustrated voters.
The Muslim Brotherhood says that security forces have systematically tried to prevent its supporters from voting.
According to the Brotherhood, more than 1300 supporters of the movement have been rounded up since the election opened on 9 November, including about 100 since Monday.
Muslim Brotherhood supporters
protest against security forces
The ruling National Democratic Party's two-thirds majority in the 454-seat parliament is not at risk, as many of Wednesday's runoffs are contested by two members of the party.
The US State Department voiced concern on Tuesday about the abuses in the electoral process, charging that they sent "the wrong signal about Egypt's commitment to democracy and freedom".
Voting will take place in remote regions such as the Sinai peninsula and Upper Egypt, but attention will be focused on Islamist strongholds in the Nile Delta, north of Cairo.