Authorities opened 174 polling stations amid stepped-up security in the central Congo's diamond-mining city of Mbuji-Mayi, where stations and voting materials were burned Sunday by people believed to be supporters of veteran politician Etienne Tshisekedi, said Hubert Tisuaka, an election official.
The European Union, Congo's former colonial ruler, Belgium, and other nations said isolated violence had not kept the elections from being free and democratic.
"We urge the Congolese population to see their peaceful participation in this process in a spirit of national reconciliation," said EU foreign aid chief Louis Michel, a former Belgian foreign minister who has treated Congo's reconstruction efforts as a top priority.
The vote was for a new president and legislature to replace Congo's transitional administration, which took power after back-to-back wars that lasted from 1996 to 2002. It was the first multiparty election in 45 years of strife and dictatorship in the country the size of Western Europe, whose people remain poor despite the country's diamond and mineral riches.
Militia fighters still rape and loot in the lawless east and the conflict kills 1,000 daily.
Electoral officials and observers outnumbered voters Sunday at many polling stations in Mbuji-Mayi. But that did not keep protesters from pelting would-be voters with stones.
Tshisekedi had called for a boycott of the elections but has not publicly instigated violence. His supporters, however, were believed responsible for more serious election-related violence at election protests in the capital, Kinshasa, that left several people dead.
He has his main base of support in central Congo.
Fresh balloting materials arrived in Mbuji-Mayi late Sunday from Kinshasa, said Tisuaka, the election official.
The party of vice president and former rebel leader Azarias Ruberwa, who was also a candidate, denounced what a spokesman called "irregularities that took place in all the country's territories" including people kept from voting because others had used their names, and ballot boxes opened by election workers instead of being delivered sealed to authorities.
Vote counting began after polls closed Sunday evening, but final results were not expected for weeks. Results will be hand-tabulated and transported to Kinshasa by plane, truck and boat.
The Belgian government welcomed what it said was a well-organized and peaceful ballot.
"This historic vote, free and democratic, was open to representatives of a wide spectrum of political opinions," a foreign ministry statement said. "The elections are very encouraging for the future."
Belgians ruled the mineral-rich nation from 1885 to 1960. Historians say several million people were either killed or died from the effects of colonial misrule.
If Tshisekedi succeeds in keeping voters from the polls, he is likely to use that as proof of his influence as he pushes for a greater say in national politics in the country formerly known as Zaire.
The failure of his supporters to register has an effect beyond Sunday's vote.
The 500 seats in the National Assembly were allocated according to the number of registered voters. Mbuji-Mayi, Congo's second-largest city, with nearly 4 million people, will have only 11 seats, compared to 58 for the 8 million residents of Kinshasa, the capital.
That could mean more marginalization for the central region, known as Kasai, which had declared secession months after independence from Belgium in 1960.
Reports from 10 polling stations in Mbuji-Mayi late Sunday indicated turnout was between five and 15 percent.