Prabowo had about 58 per cent of votes according to four pollsters, based on ballots counted in a sample of voting stations nationwide. The number of votes they had tallied ranged from about 52 per cent to 67 per cent hours after polls closed on Wednesday.
Rivals Anies Baswedan and Ganjar Pranowo had about 25 per cent and 17 per cent respectively, according to the independent pollsters that were conducting "quick counts" at the close of voting.
Anies' team said on Wednesday it had found "many violations" on election day, including vote tampering and disenfranchisement.
"We have recorded all our findings in the field," said Ari Yusuf Amir, head of Anies' legal team, adding the team was still collecting evidence.
Indonesian presidential candidate Anies Baswedan's team alleged vote tampering during the poll. (AP PHOTO)
Counts by reputable outlets have proven to be accurate in previous elections. An official result is not expected until several weeks after the vote.
The pattern could signal a first round win for Prabowo. To win in a single round, a candidate needs more than 50 per cent of votes cast and 20 per cent of the ballot in half of the country's provinces.
If no candidate wins a majority, a runoff between the top two finishers will be held in June.
The contest pits popular former governors Ganjar and Anies against the pre-election frontrunner Prabowo, a former special forces commander feared in the 1990s as a top lieutenant of Indonesia's late strongman ruler Suharto.
"Alhamdulillah (Praise be to God), we hope the election can go in one round," said Nusron Wahid, secretary of Prabowo's campaigning team, commenting on the latest quick counts.
The world's biggest single-day election has included nearly 259,000 candidates vying for 20,600 posts across the archipelago of 17,000 islands, but the focus has been firmly on the race to replace President Joko Widodo, whose influence could determine who takes the helm of the world's third-largest democracy.
The early lead will be a big boost for Prabowo, who has undergone an image rebrand and is contesting his third successive election after twice losing out to the hugely popular Widodo, who cannot run again because of term limits.
Some 259,000 candidates are competing for 20,600 posts in Indonesia's elections. (AP PHOTO)
Jokowi, as the incumbent is known, is tacitly backing and betting on his former rival as a continuity candidate to preserve his legacy, including a role for his son Gibran Rakabuming Raka as Prabowo's running mate.
Two surveys issued last week gave Prabowo just over 50 per cent support, with Anies and Ganjar 27 and 31 points adrift, respectively, though the quick counts point to a stronger lead.
"This is an emphatic result that diminishes prospects for legal challenges and will also provide the Widodo-Prabowo alliance with an element of affirmation from the public for decision-making in the months ahead," said political analyst Kevin O'Rourke.
Nonetheless, he added "concerns exist about the prospect of further incursions on democratic norms".
Former Jakarta governor Anies and ex-Central Java governor Ganjar had been trying to woo undecided voters to try to force a runoff in June.
"I want to underline that we want honest and fair elections so that it becomes peaceful," Anies said at a polling station.
Deadly riots broke out after the 2019 election, when Prabowo had initially contested Jokowi's victory.
Some 200,000 security personnel are on guard.
"So far, the situation is safe, under control," said National Police Chief Listyo Sigit Prabowo.
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