One of the darkest characters from Indonesia’s bloody past has reinvented himself as a respectable candidate for vice-president and could emerge as the country’s most powerful politician after elections next month.

He is Prabowo Subianto, 58, a former special forces commander and army lieutenant-general, who married Titiek, the second daughter of the late dictator Suharto, and was associated with the violence and nepotism of his regime.

Human rights groups have condemned his record in East Timor and Jakarta, where men under his command shot demonstrators and kidnapped opponents. Last week activists called for voters to shun him.

Prabowo refused to talk about his past when questioned by The Sunday Times last week. Over the years he has repeatedly denied all the allegations. But they will not go away.

He served four tours of duty in East Timor, where Indonesian occupation forces were accused of war crimes including torture, rape and murder. In the last years of the Suharto regime, special units under his command were blamed for abductions and disappearances of pro-democracy activists.

The Indonesian media reported widespread rumours that he organised mobs to loot, burn, kill and rape throughout Jakarta’s Chinatown in 1998 in an attempt to sow chaos and pave the way for a coup.

After Suharto stepped down, Prabowo was accused of threatening the new president, B J Habibie, by deploying his commandos around the palace.

Prabowo went into exile but has made a comeback thanks to a multi-million-dollar advertising campaign funded by his brother, a tycoon. He is standing as running mate to Megawati Sukarnoputri, who served an undistinguished term as president from 2001 to 2004.

“I would like to see Indonesia as a more prosperous and self-reliant country and to be able to better manage its resources for the benefit of the people,” he said.

Political analysts see Megawati as weak and ineffective. They believe that if she won the presidency, Prabowo would become the stronger figure.

Megawati is the daughter of Sukarno, Indonesia’s first president, while Prabowo is casting himself in Sukarno’s role as a friend of the poor.

“I realised the only way to make a difference was through the political system,” he said.

The pair are challenging President Susilo Bambang Yudhoyono, who is standing on a platform of competence and personal integrity.

President Barack Obama, who spent part of his childhood in Indonesia – the most populous Muslim nation with 210m people – is planning a symbolic visit later this year to continue improving relations between America and Islam.

The prospect that he may be greeted by Prabowo is likely to dampen the enthusiasm of White House planners.

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