Amid boycott calls as tensions over a separatist movement in Papua have increased in recent weeks, about 80 suspected separatists attacked a police post in the provincial capital, Jayapura, with arrows, machetes and spears early on Thursday morning, said Major-General Bagus Ekodanto, the local police chief.
Attackers also stabbed several motorcycle taxi drivers and burned an oil depot and property at a state university, he added.
But by midmorning the situation appeared calm, with voters forming long lines to cast ballots.
The other potential trouble spot is Aceh province in the country's western-most island of Sumatra, where a three-decade separatist war ended in 2005.
The three week campaign period leading up to Thursday's vote has been 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.
"This election is important for consolidating democratisation and providing reformers with a stronger mandate for pursuing institutional reforms, primarily in the civil service and the judiciary," Kevin O'Rourke, a Jakarta-based political risk analyst, told Reuters news agency.
Presidential polls decider
Thursday's parliamentary elections could determine if Susilo Bambang Yudhoyono, the president, will have enough support to win a second five-year term in July's presidential polls.
|Half a million polling stations will be open across the country of 17,000 islands [Reuters]
Ahead of the vote, most opinion polls put the Democratic party, led by Yudhoyono, in a comfortable lead.
The party founded in 2001 is several points ahead of more established rivals such as Democratic Party of Struggle (PDI-P), led by former president Megawati Sukarnoputri, and Golkar, the party once led by Suharto.
One survey published on Sunday by the Indonesian Survey Institute gave the Democrats 26.6 per cent, compared with 14.5 per cent for the PDI-P and 13.7 for Golkar.
If those polls prove correct, the vote will be a major victory for Yudhoyono and put him well on course for re-election as head of state in July.
However, that could be challenged if Golkar and the PDI-P decide to work together in a coalition.
The election itself is 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 are eligible to vote in the one-day affair, and those who show up will be confronted by ballot papers the size of foldout maps or roughly the width of polling booths.
|Critics say the campaign has been big on noise and colour, but short on substance [AFP]
In the run-up to the vote, the United Nations Development Programme (UNDP) has been running a multi-million dollar voter education campaign, using TV and radio commercials, public debates and even puppet shows to encourage people to vote.
Hakan Bjorkman, the UNDP's Indonesia country director, said the "get out the vote" drive was aimed at reaching out to all Indonesians, including "marginalised individuals" such as sex workers, the elderly and the disabled who are often overlooked in the campaign.
The vote is taking place at a critical time for Indonesia, with unemployment and poverty on the rise as a result of the impact of the global economic crisis.
The election campaign has, however, been criticised by some analysts for often empty sloganeering by candidates promoting their own personalities, lack of serious policy debate and widespread vote buying.
Election rallies held across the country have been colourful lively events, with music and freebies handed out to supporters, but have seen little doled out in the way of political substance.
Surveys published just days before the vote showed as many as a quarter of voters remained undecided, with many saying they could spoil their ballot papers.
And one of the president's sons is under investigation for vote buying, accused of handing out 10,000 rupiah banknotes (88 US cents) to people at a recent Democratic party rally.
"It wasn't him but his supporters doing it without his knowledge," one party official was quoted as saying.