Outside, it was burningly hot, the skies clear blue. But, inside, there was only darkness. For the next nine-and-a-half hours, in the Jerusalem Cinematheque, they would sit, rapt and in silence, through Shoah, the film made by the French director Claude Lanzmann, which was already being garlanded by critics around the world as the greatest single film about the Holocaust and one of the very greatest documentaries in the history of cinema.

It was June 1986, eight months after the film's release. Hushed audiences had sat spellbound at screenings in Paris and New York, but this June day was different. It was the first official showing of Lanzmann's masterpiece in Israel, its première marked as all but a state occasion. Taking their seats at the Cinematheque, a newly opened art-house cinema facing the walls of the Old City, were Israel's prime minister, Shimon Peres, along with the country's president, chief rabbi and chief of staff of the military. A surging pack of press and cameras had greeted their arrival.

Less noticed as they made their way through the heaving crowd were the rest of the invited audience. Among them were several of those who appeared in the film: the survivors of the Nazi death camps, the resistance fighters, those who had witnessed the slaughter up close. They were in the room. Many had their children at their side.

Lanzmann himself - a fighter in the French resistance, a former lover of Simone de Beauvoir and confrère of Jean-Paul Sartre - was agitated. Earlier that morning, Alan Reich, then an intern at the Cinematheque and now a documentary maker, had brought the director breakfast in his hotel room. "He was completely stressed out: he was sitting there, writing notes, getting up and pacing the room, popping pills to calm himself down. He was really quite anxious."

The film had been lauded everywhere, but the judgment of Israel mattered to Lanzmann especially. He was presenting his account of one of the defining events of Jewish history to the world's only Jewish country - a country whose leading officials had chosen him for the task, entrusting him with this work of memory. He was adamant that the Jerusalem audience not miss even a moment of the story he had to tell. Just before the screening, he had clashed with the Cinematheque's founder, Lia van Leer. "He said, 'there's one thing you have to know: when the film starts, you lock the door, nobody leaves,'" Van Leer recalled when I spoke to her in Jerusalem earlier this year. "I said, 'Are you crazy? If somebody has to go the lavatory, what do they do? Should they pee in their pants?'" Only when Van Leer declared that she would not forbid Israel's prime minister from visiting the bathroom, did Lanzmann relent.

At last, everyone was seated. A hush descended. The director rose to introduce Shoah - the Hebrew word for destruction, and the preferred Israeli term for the Holocaust. He said how glad he was that so many had come to see his film, a film he had made with all his heart. He headed for his own seat, but he could not stay in it. Instead, and for the duration of the screening, he was in and out of his chair, patrolling the auditorium, unable to sit still. He wanted to see the 380 faces that made up his audience.

For some, seeing the story of the Shoah played out on screen for 566 slow minutes proved too much. At one point, a member of the audience, a survivor, suffered a heart attack. He had to be stretchered away. Another fainted.

It was as if, for one extraordinary June day, Israel itself grappled with the event that preceded its birth by a handful of years, and has haunted it ever since. It did so in an unprecedentedly concentrated way: the leaders of the Israeli state were all present, together, in one room and in the dark. What the audience experienced during those hours was a reminder that Israel's relationship with the Holocaust has been impossibly tangled, stirring emotions that linger still: grief and pain, of course, but also guilt, fear and even shame. The story of the day Shoah was screened in Jerusalem is also the story of how the Shoah has reverberated, and continues to reverberate, through Israeli life.

In the politics of the country, in the way it relates to the rest of the world, the shadow of the Holocaust is never far away. It is there in the most basic argument offered for Israel's right to exist: that, after the murder of six million, Jews need a safe haven that they can call their own. It is there, too, when Israeli leaders insist that they have not only the right but the duty to crush any and every threat to the security of their citizens, because "never again" will Jews be left defenceless.

All of this hung heavily in the air at the main auditorium of the Cinematheque that day nearly 30 years ago, as Lanzmann paced among the rows, watching the faces in the dark. Staring out most keenly of all were the survivors, those who had been present at the conflagration and who had built new lives and new families in a new home - a home that had never quite known how to embrace them.

The youngest face to appear in Shoah belongs to Hanna Zaidel. She is a grandmother now, in her 60s, but on screen she is in her 20s, beautiful, taking long moody drags on a cigarette. Speaking first in Hebrew, then through a French interpreter - one of the reasons why the film is so long is that Lanzmann eschewed subtitles, insisting on consecutive translation - Zaidel tells how she learned the remarkable story of her father, Motke, in scraps, extracting one fact at a time. "I had to tear the details out of him," she says. "He was a silent man, he didn't talk to me." Addressing the camera, she adds that only "when Mr Lanzmann came" did she hear the whole story, told in one go.

When the Nazis liquidated the Vilna ghetto, in today's Lithuanian capital of Vilnius, they did it by leading an estimated 90,000 Jews eight miles to the Ponari forests and shooting them dead, en masse, letting their bodies fall into vast pits originally dug by the region's previous Russian occupiers for use as petrol reservoirs.

When the killing was over, as many as 25,000 corpses were left in each pit. Next, the Nazis sent in chain gangs made up of some 84 Jews - 80 men and four women - shackled above their calves day and night, to dig the bodies out and burn them.

One group was charged with removing gold teeth from the dead. Motke Zaidel was one of those 84, forced on pain of death to burn the corpses of his own friends, neighbours and even relatives. In Shoah, Motke Zaidel tells this story with the Israeli forest of Ben Shemen as a backdrop. In the distance, there is a bonfire, sending wreaths of smoke into the air.

When I met Hanna Zaidel this year in her home in Tel Aviv, her hair shorter and grey now, and with a picture of her late father on the sideboard, she offered an unexpected memory of him. "The main thing is that he was washing hands all the time. He was washing his hands, he was washing our hands. All the time. He was cleaning up all the time. And he kept on doing it, to my sons, to his grandchildren. So whenever they saw him, they used to hide their hands like this." She pulled her hands into her sleeves. "Until I told him, 'Daddy, their hands are clean. They don't need to clean Ponari from their hands. Please stop it.' And he did."

The Holocaust survivors - and their children - who gathered in the audience at the Jerusalem Cinematheque that day would have recognised that account and especially Motke Zaidel's reluctance to speak of his experience. It fitted well with what was then an established narrative of Israel's complex relationship with the Holocaust. The accepted view held that those who had survived were, initially at least, all but silent about the hell they had endured. Perhaps it was because they were simply too traumatised, rendered mute with pain. Perhaps they were simply determined to start afresh, to put the torments of Europe behind them and begin anew, never looking back.

The final speaker in Shoah is Simcha Rotem, one of the last surviving heroes of the Warsaw ghetto uprising. He describes how, after the liquidation, he emerged from the sewers to find himself alone in the place, now reduced to a ruin. He walked for hours in the ghetto but nothing and nobody was left: "I didn't meet a living soul. At one point I recall feeling a kind of peace, of serenity. I said to myself: 'I'm the last Jew. I'll wait for morning, and for the Germans.'" Those are the last words of the film.

Rotem was in the audience, watching himself on the screen that day in Jerusalem. Today aged 90, his eyes still sparkling with almost boyish energy, he described the significance of Lanzmann's film and why it meant so much to Israel. "Testimony was important," he said. "Telling my story, the experience in and around the ghetto first-hand, was hugely important. I think it helped people first to see at first hand that it was true, that these things really did happen, but also to think more deeply what had happened."

He left the cinema full of admiration. "Lanzmann made an extraordinary film, a film that's incomparable with anything that's been made since." Even now, Rotem is best known by his nom de guerre from the Jewish underground: Kazik. Despite his impeccable resistance credentials, in the early days of Israeli statehood, even the legendary Kazik was wary of talking too much about his past. "People had a problem understanding and digesting the story. Really hearing the story. And I felt there was sometimes a question about what we did and how we got through it. People would ask, 'How did you survive?' And what they really meant was, 'What did you do to survive?'" Tired of being viewed as a suspected collaborator, he developed a coping strategy. "When people asked where I was from, I said I was from Petach Tikva" - a town close to Tel Aviv.

A shift came in 1961, with the trial in Jerusalem of Adolf Eichmann, one of the prime architects of the Nazis' "final solution". "The Eichmann trial was a real turning-point, because it engaged the young generation, the Israeli-born generation," said the historian, Yehuda Bauer. For hour after hour, survivors were on the witness stand, describing in painstaking and painful detail what they had endured and what they were up against. But, by the early 1970s, Israeli officials, particularly those around Yad Vashem, Israel's state Holocaust memorial and museum, worried that the impact of the Eichmann trial was beginning to fade. They wanted to find a new way to communicate this formative event in Jewish history to the next generation, this time harnessing the power of cinema. The call went out to Lanzmann, a luminary of the French intellectual left.

The director was summoned to Jerusalem, where he delivered a presentation for the top brass at Yad Vashem, confining himself to "generalities", according to Bauer: "He didn't want these people to have a say in what he was doing." Nevertheless, he had done enough to impress. As Bauer put it: "You don't try to stop a genius." The director left with a promise of funding. The timing of Lanzmann's commission would prove crucial.

Ten months later, Israel would face a near-death experience, believing itself to have come close to defeat in the Yom Kippur war. The muscular "new Jews" of 1948, the conquerors of 1967, suddenly saw themselves as vulnerable.

For the Israeli journalist and historian Tom Segev, the 1973 war shifted the country's understanding of the Nazi period once again: "What it basically says is, if we [the Israelis] could hardly survive the Egyptian and Syrian armies, what do I expect of some elderly woman in Warsaw facing the Nazis?" Segev told me. "And it is at this point that the concept of heroism in Israel begins to change. It is no longer [just] someone who throws a grenade at the Nazis. It is also someone who manages to get some bread for her children, who manages to retain their human dignity. Because that's what the Nazis wanted to take away."

This was the context in which Lanzmann set to work on a project that would dominate the next 12 years of his life - and help reshape Israel's, and the world's, understanding of the Holocaust.

The length of Shoah, the demands it imposes on the audience, make it less like seeing a movie than taking part in a ritual, a sacred rite of remembrance. I went to see it with a friend, at the Curzon cinema in London, in September 1986, just a few months after the première in Jerusalem. My friend made the mistake of bringing popcorn - but he did not get very far with it. He had barely begun chomping when a woman from a nearby row leaned over and slapped him, hard, on the thigh. In an accent thick with the sound and memories of prewar Europe, she said: "Have you no respect?"

The film's pace is unsettling. There are slow, lingering shots of the (usually Polish) countryside, without commentary or music. Shoah includes no archive material at all, none of those now-stock images of skeletal inmates or corpses piled into small mountains. There are no interviews with politicians or government ministers. Instead, it focuses on the ordinary people who were caught up in a period of collective human wickedness, in which cruelty became a system and day became night. The film listens as they describe it, detail by murderous detail.

The effect is mesmerising. Zaidel recalled the extraordinary hush inside the Cinematheque: "It was very strong, people sitting for so many hours… Even the flies didn't want to fly there. You didn't hear anything."

There was little of the usual shifting in seats, despite the marathon length of the film. People stayed still, riveted. Nevertheless, and despite Lanzmann's edict, some did have to take a break. One woman went to the bathroom just to wash the tears off her face. Another went outside and found herself dazzled by the sunlight: it was a shock after the darkness and the crematoria and the death. But when they went back inside the auditorium, Shoah was still going on. Because that is how it was: for at least four years, the killing did not stop. Between 1941 and 1945, no matter what else was going on in the world, the wheels of death were still turning. Somehow the very form of Shoah conveyed something important about the reality of the event itself.

For many in that audience it was overwhelming. Shimon Peres, the prime minister at the time, had to leave before the film was over. But it was more than diary commitments that took him away. "I couldn't stay," he told me from his office, which overlooks the Jaffa coast. "I felt like a broken man." Now in his 90s, the film took him to his childhood in prewar Poland. "These were the people with whom I lived. There was nothing imaginary about it. It was very hard. [Afterwards] we didn't know what to say to each other. All of a sudden, words lose their meaning. They look so pale."

For some critics, it was excessive. Tom Segev faulted the film for adding drama to an event that needed no added drama. He disliked the way Lanzmann staged certain scenes, demanding for example, that a man who, as a boy, had been forced by the Nazis to sing a particular folk song, sing the song again, for the cameras. Others resented the director's probing, relentless style. For one sequence, involving Abraham Bomba, a former inmate of Treblinka and a trained barber, Lanzmann recreated a barbershop, in Tel Aviv - and interviewed Bomba as he cut the hair of an unidentified customer. In English, in a voice at first oddly matter-of-fact, Bomba combs and clips as he explains that he and his fellow barbers were forced to cut the hair of women as they entered the gas chambers. The women did not know what was about to happen to them. They believed they were "getting a nice haircut". (Their hair was, in fact, collected and sent to Germany for commercial use.)

Bomba then recalls how, one day, a transport arrived from his hometown of Czestochowa. "I knew a lot of them. I lived with them and some of them were my close friends. And when they saw me, they started asking me… 'What's going to happen to us?' What could you tell them? What could you tell them?" He goes on to say that a fellow barber suddenly saw his own wife and sister enter the gas chamber." At that point, Bomba, previously so controlled, so fluent, halts.

"I can't," he says. "It's too horrible. Please." He pauses for about 90 seconds. Lanzmann's camera remains on Bomba's face. We watch as the armour a man has built to protect himself over the intervening four decades crumbles before our eyes. Bomba seems to be breaking. "I won't be able to do it," he pleads.

"You have to," Lanzmann says.

"Don't make me go on. Please."

It is one of the most painful sequences in the film. There can be few more affecting scenes in cinema. But for the audience watching on that scorching day in Israel, it would have carried an extra power. The room was packed with survivors who knew Bomba's anguish, even if their experience had not been as extreme or as morally devastating as his. And what they saw on the screen was not black-and-white footage from faraway Europe. They saw a man in contemporary Tel Aviv, tanned and wearing a summer shirt. Yet, slowly, that exterior - the carapace of the confident, brash Israeli - was peeled away, to reveal a Jew trembling with grief and pain.

This gets close to the heart of what was singular about Lanzmann's film. If it had a message, it was that the Holocaust was not in the past: it still existed in the present. It did not exist only in archival monochrome, but in colour, in the here and now. The places where it happened were not in some distant galaxy. They happened in this world: in this forest, in this field, in this village. And its pain lives on in this world, too, in the places where the victims are remembered and the places where the survivors fled. The Holocaust runs deep in the soil of Poland and Germany and Lithuania and Belarus and every place Jews were killed, of course. But the Bomba sequence, like the shots of Motke Zaidel in the Ben Shemen forest, told that Israeli audience watching in Jerusalem that the Shoah was alive in their country, too. They could not escape it. Too many people, and too many of their children, had been shaped - or broken - by it.

Jonathan Freedland's radio programme 'Shoah In Jerusalem' can be accessed via the BBC iPlayer. The above is an abridged version of an article that first appeared in the Guardian