Stephen Fitzpatrick, Jakarta – Retired army general Prabowo Subianto has threatened legal action after coming second in Indonesia's presidential elections, which he branded "far from democratic".

General Prabowo, who is tarnished by human rights abuse allegations relating to the 1998 fall of former dictator Suharto, claimed the likely existence of millions of incorrect names on the electoral rolls made the results invalid.

In Wednesday's nationwide poll, the incumbent, Susilo Bambang Yudhoyono, was returned in a landslide.

Although official results are not expected until the end of the month, a range of respected "quick count" organisations all put the result for Dr Yudhoyono and his running mate, economist and former central bank chief Boediono, at more than 60 per cent.

General Prabowo, running as the vice-presidential candidate on a ticket headed by former president Megawati Sukarnoputri, held a press conference late on Wednesday night to declare the team's intention to pursue the matter in the courts.

"We've conducted an election with a voter roll that had problems, and yet the election was allowed to continue," he said.

"We had already warned and pleaded with the electoral commission to resolve this matter, but they did not. We understand that there has been widespread fraud in all regions (of the country)."

The Megawati-Prabowo team appears to have won about 27 per cent of the popular vote, based on the quick-count results.

The third place-getters, current Vice-President Jusuf Kalla and retired army general Wiranto won less than 13 per cent and applauded the winners yesterday.

"As head of the JK-Wiranto campaign team, I express congratulations on the election of SBY-Boediono," campaign official Fahmi Idris said.

There had been widespread concern at the lack of accuracy on voter lists, a circumstance partly brought about by laws that restricted the electoral commission's budget and therefore its ability to cross-check data.

However, this week's Constitutional Court decision allowing people greater access to voting booths largely took the heat out of that issue.

Political analyst Anies Baswedan said yesterday that discrepancies between initial exit polling and the later quick count indicated many people had voted for the Megawati-Prabowo ticket "but did not want to admit it".

"Perhaps they felt under some pressure. However, it's clear that Prabowo also contributed in a large way to the result, since on her own Megawati was not polling above 20 per cent," Dr Baswedan said.

As General Prabowo and his billionaire campaign manager brother, Hasyim Djoyohadikusumo, made their claims of fraud, they were being investigated for breaking the election law.

The national electoral watchdog, known by its Indonesian-language acronym Bawaslu, said yesterday that it wanted General Prabowo and Ms Megawati to explain why they had held a televised press conference the day before voters went to the polls.

Under laws governing campaigning, all candidates are required to engage in "days of calm" from several days before the polls are held.

However, the pair made a last-minute attempt to attract voters, inviting television reporters to Ms Megawati's central Jakarta home where she gave a demonstration of how to make "soto", or traditional Indonesian soup.

It was a telling display from someone who has often been seen by her critics as better suited to the role of housewife than that of national leader.