One of Cambodia's leading journalists and foremost researchers on the Khmer Rouge has told the Guardian he fears for his life after a two-year harassment campaign by state security forces he claims are attempting to prevent him from completing his latest film about the Killing Fields.

Award-winning film-maker Thet Sambath – whose 2009 documentary about the Khmer Rouge, Enemies of the People, was shortlisted for an Oscar – claims that uniformed soldiers and plainclothes "spies" working for the Cambodian government have repeatedly followed, harassed and chased him by car and motorbike, with the intention of "making [him] disappear".

"They are concerned I will reveal their true crime [through the new film] and … [that] their reputation will be destroyed," Sambath said. "I know too much about what really happened. They want me dead."

Sambath, a senior reporter for the Phnom Penh Post, said the harassment started in May 2010 after news reports circulated internationally about Enemies of the People. Largely regarded as a political and historical watershed, it is the only Khmer Rouge documentary with testimony from the regime's no 2 and ideological leader, Nuon Chea, whom Sambath spent 10 years tracking down and interviewing.

In the film, Chea admits he and Pol Pot decided to "kill and destroy" party members they considered enemies of the people, while lower-ranking cadres demonstrate, in graphic detail, how they implemented orders to slit the throats and dump the bodies of those targeted.

The film created a huge stir abroad and locally, winning the Sundance jury prize as well as some 30 other awards, and stimulating dialogue about a traditionally taboo subject in Cambodia itself. But Sambath's follow-up film poses a greater concern for the future of the nation, he says.

"The first film explained 'how' the Khmer Rouge did the killing, now this film looks at 'why'," says Sambath, 45, of the tentatively titled Suspicious Minds. "And the answer is not the same as what the Cambodian government has been telling the public for all these years. The real story is politically huge. It will make everyone in Cambodia come out and talk, and the government will have to explain why they lied."

Pol Pot has long been regarded as the mastermind behind the genocide that claimed nearly a third of Cambodia's population by 1979. Through interviews with regional and senior former leaders, Suspicious Minds, however, argues that it was caused by political infighting within the party, with attempted military coups and assassinations, and massacres in villages aimed at creating an unstable government and ousting Pol Pot from office.

"The reality is that the party was split beforehand and the split of the party caused the Killing Fields," says Rob Lemkin, an Oxford-based film-maker who co-directed Enemies of the People and is producing Suspicious Minds.

In uncovering the truth about the brutal regime which, in its short reign from 1975-79, killed off 1.75 million people, Sambath says he has turned himself into the unwitting target of a government still manned by former soldiers. He says he has faced police checkpoints outside his house in Phnom Penh, intimidation from armed thugs and "car chases like in Hong Kong films" deep in the wilds of rural Cambodia, where he conducts most of his interviews.

The government aim, he says, is to make him a victim of kidnap, robbery or car accident – events that are difficult to prove aren't just the result of bad luck. The government says it is unaware of his case.

In one incident, Sambath says he was pursued down a dusty country road by gun-wielding men in two cars and on two motorbikes; in another, Sambath and his two passengers were chased at speed at night on an empty rural highway, where, unable to outdrive their pursuers, they abandoned their vehicle and ran for cover in a cornfield. They hid there for three hours until their would-be assailants gave up their search. "On three separate occasions, I thought I was a goner," Sambath says slowly, his hands trembling and his voice low. "Fear is always in my heart. I am worried where I am going, who is behind me, watching me, following me."

Sambath has long kept a low profile, frequently moving house, using false names and changing schedule. His interview with the Guardian took place in five locations in two provinces over three days. Even his wife and two children are often unaware of his exact whereabouts and work projects – simple precautionary measures to keep them safe, he says, as police reports he has filed regarding the harassment have been inadequately investigated.

Now Sambath spends much of his time in and out of hospital for shortness of breath and heart palpitations that he thinks are directly related to stress. He has had to suspend work on the second film until his health improves.

While Cambodia is celebrated for having a freer press than its south-east Asian neighbours, Sambath's case of intimidation and harassment is not unusual, according to Phil Robertson, of Human Rights Watch, who says that journalists in Cambodia often face threats, assaults, arrests, imprisonment and staged "accidents".

"Culpability for Khmer Rouge atrocities is one of the real electric wires of Cambodian politics," Robertson says. "But it is also part of everyday Cambodian governance that people with power feel no compunction … to silence people who may bring out an unpleasant or inconvenient truth about them, whether it be about corruption or the political dynamics of how the Khmer Rouge insurgency ended."

Even the Cambodian government itself openly admits that local reporters face intimidation from "bad people" and stresses that, while it promotes measures to protect their safety, journalists must keep their wits about them.

"Everywhere on Earth there are good people and bad people – and not all policemen are good," said government spokesman Phay Siphan. "You have to be intelligent to figure out where is safe, who gives you a hard time, and who will protect you … [But] we are a safe country and we take this very seriously. There are laws in this country to maintain freedom of expression."

Tension surrounding the Khmer Rouge and its brutal past is at an all-time high after an international tribunal last month sentenced former torture prison leader Kaing Guek Eav, known as Duch, to life imprisonment. It is now trying Nuon Chea, along with two other former heads of state, for war crimes. From villages to government offices, Cambodians are wondering who will be next, with many choosing to break their own silence and learn more about the past.

Born to farmers in a thatched-hut village on the edge of the jungle 100km from north-west Cambodia's largest town, Battambang, Sambath lost both parents and a brother to the ultra-communist regime and spent four years with some 2,000 other children in a work camp, where he survived on a handful of gruel a day.

After Vietnam liberated the country in 1979, Sambath fled through a battle between Khmer Rouge and Vietnamese soldiers and ended up in a refugee camp in Thailand, where he learned English. After returning to Cambodia in 1990, he worked as a freelance UN translator and then reporter for the English-language papers Cambodia Daily and Phnom Penh Post.

"But I never understood what happened," Sambath says. "We had no answers from the top commanders about what and who was behind the killing. Why did so many Cambodians die under the Khmer Rouge? So I found a few low-ranking cadres, became friendly, and started asking questions." He dedicated his weekends to his "project", driving thousands of miles across the country on a tip-off to find a single former soldier, sleeping at cheap roadside inns and travelling with his belongings in nothing more than a black plastic bag. Within a decade, Sambath had interviewed 1,000 former Khmer Rouge soldiers and leaders, logged more than 1,000 hours of video footage, and spent more than $10,000 (£6,300) of his own money.

"Everything goes to the project; I pity my family," he says. "Once this is over, I will tell my children why we never go on holiday, and why my wife never has any new clothes or nice jewellery. I hope they understand."

While Sambath plans to escape from Cambodia before the second film is released, he has not yet told his family the news. He knows his time is limited and that he must work fast. "We have nothing now. We rent our house. We have no cash. If they lose me, they won't be able to survive." Lemkin calls Sambath a "marked man" but says he has no choice but to finish what they both call a "historical obligation" to Cambodia. "This is the biggest story in Cambodia and one of the biggest stories in terms of mass violence of the 20th century," says Lemkin. "But for Sambath, there simply is no other story. This … defines his life and explains the experiences of his life. So he is prepared to never give up."