Election officials ordered a national vote recount after early results showed "tens of millions" of votes might have been spoiled in Monday’s inaugural presidential elections.
The ballot papers were packaged in such a manner that if the ballot was not unfolded properly, voters punched through both sides of the paper, rendering the ballot invalid, the National Election Commission said.
"There were reports from a number of different places in the country and we took immediate steps to improve the situation," National Election Commission (KPU) chairman Nazaruddin Sjamsuddin said late on Monday.
"I believe there might be tens of millions of invalid ballot papers."
It is not immediately clear what effect the recount will have as organisers said last week they did not expect a final election tally before the end of next week.
Results based on nine per cent of the 153 million eligible voters showed incumbent leader Megawati Sukarnoputri in second running with 26.6% of the vote, according to official tallies on the commission's website on Monday.
In third place was former armed forces chief Wiranto with 23.3%. Two other candidates were further behind.
The two top vote-getters will go head to head in a September run-off, because neither won more than 50% of the electorate.
While anecdotal evidence from polling stations in several areas of the country suggested turnout is down from the 84 per cent participation in April’s legislative election, paper gremlins did nothing to dampen enthusiasm at the polls.
"The Euro 2004 football match finished very early in the morning and I really want to go to sleep," said shopkeeper Suparman, who was lounging with friends beneath the red-and-white awning of a central Jakarta polling station.
Incumbent President Megawati
has struggled to reach a run-off
"But we'll stay here until we know the results. This is the first time we do this so it is a historic day."
In a canal-side slum 22-year-old Benny was strumming a guitar and chatting with friends.
"I don't know if it is going to make a big difference who we vote for, but I still think it is important because for so many years we lived with a dictator," said Benny, one of an estimated 22.8 million first-time voters. "It's important to show we support democracy even if we don't support the candidates."
Earlier, millions of people across the world's largest archipelago voted in Indonesia's first direct presidential election as Yudhoyono warned of possible violence if the contest extended to a second round.
Yudhoyono, 54, also warned of possible cheating.
"Politics is tough and cruel. Sometimes for power any means can be used," he said.
He has complained of a smear campaign, spread by SMS messages across the world's most populous Muslim nation, which falsely alleges he is a Christian.
In the dying days of the campaign Yudhoyono said he worried that "cities will burn" if the elections are not settled in the first round.
"It is very important for SBY to win in the first round," said Daniel Sparingga, a political scientist at Airlangga University in Surabaya.
"If he doesn't, there could be tensions between the political elite and questions among the people on the street. Only one-third of people realise there could be another round. Even if he doesn't get 50 per cent of the vote, there will be an expectation among many of SBY's supporters that he will become president."
Among the poll observers was
US ex-president Jimmy Carter
Even the United Nations is quietly concerned about the results of these elections, particularly if the incumbent president fails to make it through to the second round. A closed meeting between senior UN department heads last month focused on several possible scenarios in the wake of a deadlock.
"Basically the feeling is that because we've got a 70 per cent turnover in the legislative seats, the outgoing members are going to want to pad their wallets before they leave," said a UN staffer who attended the meeting.
"The fear is that without tough leadership, they will use the time between now and the swearing-in of the new government in October basically to loot the treasury."
Yudhoyono's astonishing rise in popularity has been the most marked feature of this election year.
Megawati, despite being a daughter of charismatic founding president Sukarno, appears aloof and uncommunicative.
By contrast, Yudhoyono projects a soothing image of firmness, calmness and courtesy. In the public's perception, he is untainted by allegations of human-rights abuses which dog the other ex-military candidate Wiranto.