President Susilo Bambang Yudhoyono's Democratic Party is expected to do well, which could help the former general in his re-election bid.
Polling stations closed at noon today (5 GMT), but since the country is spread over several time zones, voting continued.
The complex electoral system complicates matters. Voters directly choose a single candidate, not a party.
Accusations of vote exchanges and rigging have been made as a result of the slow counting in the country’s more than 500,000 polling stations that are strewn across the vast archipelago.
Violent incidents have also been reported yesterday. In the city of Jayapura, capital of Papua province, about a hundred people, armed with spears and machetes, stormed a police station; six people died and several more were wounded.
Law enforcement also found about ten bombs and arrested 15 people.
The attack was blamed on local separatist movements active in the province for many years.
Some analysts expect the Democratic Party to win 26 per cent of the popular vote, a result which would allow President Susilo to run in the upcoming presidential election without support from outside his party.
Surveys indicate that the Indonesian Democratic Party of former President Megawati Sukarnoputri should get 14 per cent of the vote, followed by Golkar, the party of former dictator Suharto, at 13 per cent.
The four Islamic-based parties came in at around 4 per cent each.