Early results showed a close race between Indonesia's Democrat and Golkar parties, dealing a potential blow to the re-election hopes of Susilo Bambang Yudhoyono, the incumbent president.
Opinion polls had put Yudhoyono's Democrats well in the lead before the vote.
The vote will determine the make-up of the national parliament and who can run for president in the more important presidential elections scheduled for July.
More then 13,000 candidates are competing for 132 seats in the upper house of parliament and 560 seats in the lower house.
In one of the incidents in Papua province, police shot dead a man when about 100 people armed with arrows and bombs attacked a police station in Papua province, officials said.
Calls for Papuan independence have grown louder ahead of the elections and Bagus Eko Danto, the Papua police chief told the AFP news agency that the incidents were aimed at "sabotaging" the election.
"The incidents ... indicate that there are people who want the elections to fail," he said.
Pro-independence sentiment runs high in Papua, which sits on the western end of New Guinea island and is mainly populated by ethnic Melanesians.
Indonesia took formal control of the region in a 1969 UN-sponsored vote by select tribal elders, widely seen as a sham and the area has seen a long-running insurgency waged by pro-independence fighters.
Celebration of democracy
Thursday's parliamentary election was only the third democratic vote since the autocratic Suharto regime was pushed from power in 1998 amid student protests.
|The elections will determine how much support the president still posseses [AFP]
The three week campaign period leading up to the vote was billed as a celebration of the Indonesia's young democracy, with towns and cities decked in colourful flags of the 38 competing parties.
But the vote is also expected to usher in a downsizing of the Indonesian political scene, with many of the smaller parties likely to fail to win the 2.5 per cent vote threshold to secure a place in parliament.
The parliamentary elections will also determine if Yudhoyono, the Indonesian president popularly known as "SBY", will have enough support to win a second five-year term in July's presidential polls.
Ahead of the vote, most opinion polls put his Democratic party in a comfortable lead – but early counts from across the country showed that lead slashed, putting the party level with the rival Golkar party, the former political vehicle of the Suharto presidency.
The election itself was a mammoth logistical exercise involving tens of thousands of security personnel and about half a million polling stations spread across an archipelago nation of more than 17,000 islands and three time zones.
About 171 million Indonesians were eligible to vote in the one-day election, and those who showed up were confronted by ballot papers the size of newspapers or roughly the width of polling booths.