The Muslim Brotherhood in Egypt has accused the authorities of harassing its candidates and committing widescale irregularities during Monday's voting.
Egyptian riot police outside a polling station near Cairo
Egypt is holding the first round of elections for the upper chamber of parliament, the Shoura Council.
Earlier, one man was killed in violence outside a polling station.
Reports say that riot police blocked access to some polling stations and the Brotherhood says many of its supporters have been beaten up.
It alleges that at some stations ballot boxes were stuffed full before voting opened, witnesses say.
Reporters at a village outside Cairo say they saw riot police sealing off a polling station and telling people there was no election there.
Independent election monitors said they were barred from entering polling stations.
"The trend has been that all the stations where Islamists are running have been closed and observers were barred from entering," election monitor Tarik Zaghlul from the Egyptian Organisation for Human Rights told the AFP news agency.
Egyptian government rejected the Brotherhood's accusation and the criticism, saying the elections were free from interference.
An opposition supporter was killed when gunfire broke out during clashes between ruling party supporters and independents outside a polling station in the northern Nile Delta region, police said.
The poll comes after the recent arrests of about 700 members of the Muslim Brotherhood, Egypt's main opposition force.
The Brotherhood is banned as a party, but it fields candidates as independents and is fighting for 18 of the 88 seats up for grabs on Monday.
There are 264 seats in the upper house, which has very limited legislative powers; 176 are elected in two tranches and 88 appointed by the president.
These are the first elections to be held in Egypt after changes to the constitution aimed in part at limiting the electoral chances of the Muslim Brotherhood, our correspondent says.
A military trial is currently more than 40 members of the Brotherhood, including senior members of the group.
The constitution has been changed to ban political activity based on religion and to weaken judicial supervision of elections.
Two major opposition parties, the al-Wafd and Nasserites, are boycotting the elections.
The National Democratic Party of President Hosni Mubarak has an effective monopoly power in Egypt, but this is being chipped away by the Muslim Brotherhood.
In 2005, the Brotherhood won nearly a fifth of the seats in the lower house of parliament.