For more than a year I have been presenting my film, The Act of Killing, to audiences around the world. The documentary investigates how 500,000 Indonesians were murdered in the 1950s and 60s, at the hands of a government that is still in power. Often after screenings, viewers approach me to say they had been afraid to see the film, because they'd heard the film is graphically violent – one commentator has even likened it to a snuff movie – or that survivors play themselves in re-enactments. Then they tell me they're glad they came, because neither of those things are true: the film is not violent, and all those appearing in the re-enactments are perpetrators, paramilitary leaders, and their immediate family members – that is, there are no survivors in the dramatisations. And there are certainly no scenes documenting actual physical violence. Viewers recognise that, while the film is emotionally impactful, it is not viscerally impactful or violent.

Making The Act of Killing, I spent eight years collaborating with survivors of a genocide to expose a present-day regime of fear, corruption and thuggery that the killers have built – and over which they continue to preside. When you spend so long working with survivors to expose the horrors they continue to face, the last thing you want is somehow to repeat the violence you intend to counter and expose. For that reason, it was a principle that there be no survivors in any of the re-enactments.

This was particularly important for me given the film's genesis. The Act of Killing began as a documentary about survivors, not perpetrators: survivors asked me to make a film with them about why they are afraid; about what it's like for them to live with former death squad leaders all around them, still in positions of power, with the threat that this could happen again at any time. This was in early 2003, but the army, which is stationed in every village in Indonesia, found out what we were doing and threatened the survivors about participating. The survivors urged me: "Before you give up and go home, try to film the perpetrators. They may tell you how they killed our relatives." I did not know if it was safe to approach the killers, but when I did, I found all of them to be boastful, immediately recounting the grisly details of the killings, often with smiles on their faces, in front of their families, even their small grandchildren. With this contrast between survivors and perpetrators, I felt I'd wandered into Germany 40 years after the holocaust, only to find the Nazis still in power.

When I showed this material back to those survivors who wanted to see it, and to the broader Indonesian human rights community, many people would say something like: "You are on to something terribly important. Keep filming the perpetrators, because anybody who sees this will be forced to acknowledge the rotten heart of the regime the killers have built."

From that point on, we felt entrusted by the survivors and human rights community to do a work that they could not safely do themselves: I spent two years filming every perpetrator I could find across North Sumatra, working from death squad to death squad up the chain of command, from the countryside to the city. Everybody was boastful, everybody would invite me to the places where they killed, and launch into spontaneous demonstrations of how they killed. Often, they would complain that they had not thought to bring along a machete to use as a prop, or a friend to play a victim.

We developed the film's central concept – allowing perpetrators to make fiction scenes about the killings – not as a trick to get these men to open up, but in response to their boastful openness, and as a means to understand its motives and consequences. Our "pitch" was straightforward: "You have participated in one of the biggest killings in human history," I would say. "I want to understand what it means to you and your society. You want to show me what you've done. So go ahead, in any way you wish. I will also film you and your fellow death-squad veterans discussing what you want to show and, just as importantly, what you want to leave out. In this way, we will be able to document what this means to your society, and what it means to you." I understood instinctively that if we could show how these men wished to be seen, we would also glimpse how they really see themselves, and the whole façade that genocide is heroic would come crumbling down.

Throughout those two years of filming, I was in constant dialogue with the survivors and human rights community. Anwar Congo, the film's main character, was the 41st perpetrator I filmed.

Perpetrators in film normally deny their atrocities (or apologise for them), because by the time filmmakers reach them they have been removed from power, and their actions condemned and expiated. Here, I was filming perpetrators of genocide who won, who built a regime of terror founded on the celebration of genocide, and who remain in power. They have not been forced to admit what they did was wrong. There is a "surreal normalcy" to their boasting, as Jeffrey Winters, a Northwestern University professor of Indonesian politics recently wrote, "[because] the men in The Act of Killing are not afraid – they are feared … They either received a hero's burial with full state honours if they were the commanders, or they thrived as celebrated local heroes like Anwar Congo if they were the minor thugs doing the actual killing (as in North Sumatra)."

It is in this sense that The Act of Killing is not a documentary about a genocide 50 years ago. It is an exposé of a present-day regime of fear The film is not a historical narrative. It is a film about history itself, about the lies victors tell to justify their actions, and the effects of those lies; about an unresolved traumatic past that continues to haunt the present.

The film has had exactly the impact the survivors hoped for. It has been screened thousands of times in Indonesia, and is available for free online. This has helped catalyse a transformation in how Indonesia understands its past. The media and public alike are now able, for the first time without fear, to investigate the genocide as a genocide – and to debate the links between the moral catastrophe of the killings and the moral catastrophe of the present-day regime built, and still presided over, by the killers.

In October 2012, Indonesia's most important news publication, Tempo Magazine, published a special double edition dedicated to The Act of Killing, including 75 pages of boastful perpetrators' testimony from across Indonesia. The magazine's editors gathered this testimony to show that the film could have been made anywhere in Indonesia, that there are thousands of feared perpetrators enjoying impunity around the country, and that the problems of corruption and gangsterism are systemic. This special edition broke a 47-year silence about the genocide in the mainstream media.

Indonesia's National Commission on Human Rights issued its statement about the film: "If we are to transform Indonesia into the democracy it claims to be, citizens must recognise the terror and repression on which our contemporary history has been built. No film, or any other work of art for that matter, has done this more effectively than The Act of Killing. [It] is essential viewing for us all."

The opponents of the film inside Indonesia are limited to apologists for the atrocities, including the military and paramilitary thugs, who continue to violently attack gatherings of survivors across Indonesia. A paramilitary group has attacked newspapers supporting the film, and I cannot return safely to Indonesia.

For a long time, the Indonesian government ignored The Act of Killing, hoping it would go away. When the film was nominated for an Academy award, the Indonesian president's spokesman acknowledged that the 1965 genocide was a crime against humanity, and that Indonesia needs reconciliation – but in its own time. While this was not an embrace of the film, it was incredible, because it represents an about-face for the government: until then, it had maintained that the killings were heroic and glorious.

It has been moving to witness audiences around the world discover, through moments of identification with Anwar Congo, that we are all closer to the perpetrators than we like to believe. There is a scene in The Act of Killing in which I accuse Adi Zulkadry of committing war crimes, and he responds by accusing the west of hypocrisy, noting that the US slaughtered the native Americans. More to the point, the US and the UK helped engineer the Indonesian genocide, and for decades enthusiastically supported the military dictatorship that came to power through the slaughter.

When The Act of Killing was awarded a Bafta, I used my acceptance speech to note that neither the UK nor the US can have an ethical relationship with Indonesia (or so many other countries across the global south), until we acknowledge the crimes of the past, and our collective role in supporting, participating in, and – ultimately – ignoring those crimes.

Recently, we were able to make similar points on Capitol Hill. We screened the film at the Library of Congress for senators, members of Congress and their staff. The screening was introduced by Senator Tom Udall of the foreign relations committee, and afterwards, visibly moved, the senator told US News and World Report: "The United States government should be totally transparent on what it did and what it knew at the time, and they should be disclosing what happened here."

We still hope that the Indonesian government will finally acknowledge the 1965 genocide – and the present-day regime of fear built on it – as a moral catastrophe. We hope that the renewed attention to the film will encourage ordinary Indonesians to demand that their leaders be held accountable for their crimes. And we hope that it will inspire all Indonesians to work together for truth, justice, and reconciliation.