Minutes after James Leong and Lynn Lee arrived in Jakarta to present their documentary on East Timor, Passabe, at a film festival, they were told it had been struck off the programme.

Given the subject, it is easy to understand why the Indonesian authorities were concerned.

The documentary focuses on the hearings of East Timor's Commission for Reception, Truth and Reconciliation concerning Passabe, a hamlet in the Oecussi enclave where residents – many of whom were members of the local pro-Indonesia militia – killed 74 men from neighbouring pro-independence villages after East Timor voted to become independent in September 1999.

The hearings, sponsored by the United Nations to heal the country's wounds after the period of instability at the end of the 1990s, were never intended to punish the perpetratrors of the serious crimes such as murder or rape, say the filmmakers, who were invited by the UN to cover the proceedings.

The hearings turned "quite explosive" when a villager confessed to killing a man.

Passabe chronicles the horrors, featuring chilling testimonies from both the perpetrators and the victims. The filmmakers were taken to the killing fields where the villagers were allegedly tortured and massacred. But the film also attempts to illustrate the uncertain future for the country. Lee says its problems have dropped "off the radar" as the world zeroes in on the strife in the Middle East.

"Everybody [in the villages] is sick and tired of fighting, but there is a simmering resentment there," says Lee. "There's a lot of deep sadness because there's a sense that justice may never happen." This was partly because of the difficulty in getting hold of many of the militia leaders who escaped to Indonesian-held West Timor and punish them.

While the film was not allowed to be shown in Indonesia, it has received glowing reviews at the festivals where it did run. When shown in Singapore, Indonesian students were among those who praised it the most, Leong said. The Sundance Institute Documentary Fund also backed the film with a grant.

What excited Leong and Lee, however, was the February screenings in East Timor. High water levels however, prevented them from taking the film back to its subject village, Passabe.

The acclaim the film received has been a relief for the first-time filmmakers, who have worked in television production. Lee studied law but went into media work, while Leong harks from a film-making family: his father, the British-born director Leong Po-chih, was part of Hong Kong's new wave in the late 1970s with output such as Jumping Ash.

Leong Snr – who was listed as post-production consultant on the film's credits – had been "generous" in providing advice, said the son. His father suggested injecting Passabe with "cinematic" touches, which helped greatly.

Visuals aside, Passabe works because of Lee and Leong's success in getting close to the subject, including spending almost a year living in the villages.