A former rebel commander recounts the torture meted out by India to surrendered militants. guardian.co.uk

One sodden evening in April 2010, an Indian army major from the 4 Rajputana Rifles arrived at a remote police post where the mountains gather in a half-hitch around Kashmir, India's northernmost state. Major Opinder Singh "seemed in a hurry", a duty policeman recalled. Up in the heights of the Pir Panjal range, down through which the major had descended, it was snowing and his boots let in water. "The officer reported that the previous night his men had killed three Pakistani terrorists who had crossed over into our Machil sector," the policeman recalled. "Where are the bodies?" the policeman had asked, filling in a First Information Report that started a criminal enquiry. "They were buried where they were shot," the major retorted, before taking off in his jeep.

"It was not unusual," the policeman later told investigators, when questioned as to why he had not insisted on viewing the corpses or checking the identities. Kashmir had been in turmoil since Partition in 1947 and on a virtual war footing for the past two decades, with some estimates placing the dead at 70,000. Strung with razor wire and anti-missile netting, the state had been transformed into one of the most militarised places on earth, with one Indian paramilitary or soldier stationed for every 17 residents. The Pakistani intelligence services and military trained and funded a legion of irregulars, who infiltrated over the mountains to kick-start a full-blown insurgency in 1989, keeping the Indian-ruled portion of the Muslim-majority state permanently alight.

Once picture-perfect, a place of pilgrimage for backpackers and mystics of all religions, Kashmir had become one of the most beautiful and dangerous frontlines in the world. Machil, the sector in which Singh had sprung his operation, was especially treacherous, consisting of a clutch of isolated villages strung along the Line of Control (LoC), a high-altitude ceasefire line that had split Kashmir in 1972. Up here in the thin air, India had created a fearsome barrier, made lethal with the help of Israeli technology, a partially electrified series of fences connected to motion detectors, surrounded by a heavily mined no-man's land.

On 30 April, 2010, an armed forces spokesman in Srinagar, Kashmir's summer capital, confirmed Singh's story. "Three militants have been killed in a shootout," said Lieutenant Colonel JS Brar, detailing how three AK-47s, one Pakistani pistol, ammunition, cigarettes, chocolates, dates, two water bottles, a Kenwood radio and 1,000 Pakistani rupees had been recovered. The standard-issue infiltration kit. The corpseless triple-death inquiry was an open and shut case.

However, a few days later, at Panzalla police station, 30 miles from Machil, a simple missing case was causing everyone problems. Three Kashmiri families from nearby Nadihal village had turned up to report the disappearance of their sons: Mohammad, 19, Riyaz, 20, and Shahzad, 27, an apple farmer, a herder and a labourer. They had not seen them since 28 April and would not be calmed by detectives. Soon, their appeals drew the attention of Kashmir's most dogged human rights lawyer, Parvez Imroz, whose response to what would become known as the "Machil Encounter" was about to create a watershed in Kashmir.

Dressed in the uniform of the Kashmiri bar, a crisp white shirt and sombre morning suit, over the past two decades Imroz had become a fixture at the high court in Srinagar, filing thousands of habeas corpus actions (which literally translates as "produce the bodies") on behalf of families who claimed their relatives had vanished while in the custody of the Indian security forces.

These actions rarely succeeded, the Indian army insisting that the missing had flitted over the LoC to Pakistan, recalling historic scenes at the start of the insurgency that terrified New Delhi, when tens of thousands of young Kashmiris jumped aboard buses manned by youthful conductors shouting: "Pakistan, Pakistan here we come." But what the writs did achieve was to create a paper trail from which Imroz was able to estimate that 8,000 Kashmiri non-combatants had vanished from army custody in a state the size of Ireland – four times more than disappeared under Pinochet in Chile. "The military grip has been suffocating," he told the Guardian, "and making someone vanish sows far more fear than spilling their blood".

Imroz had spent much of his career facing down security forces protected by specially drafted laws. Under the Armed Forces Special Powers Act, soldiers and paramilitaries enjoy total immunity from prosecution, unless the ministry of defence sanction their trial. Using new Right to Information (RTI) laws, Imroz obtained confirmation that despite the fact that hundreds of soldiers stood accused of murder, rape and torture, not a single case had proceeded. In contrast, Kashmiri citizens are dealt with using the Jammu & Kashmir Public Safety Act, under which they can be jailed, preventively, for two years, if deemed likely to commit subversive acts in the future, with an estimated 20,000 detained, according to Human Rights Watch.

Imroz's campaigning achieved other things. He caught the attention of the UN, and this year Christof Heyns, a special rapporteur on extrajudicial executions, warned India that all of these draconian laws had no place in a functioning democracy and should be scrapped. The price for confronting the security forces and the militants they faced down was severe. In 1992, Imroz mourned the loss of his Hindu mentor, an activist who was gunned down by Muslim insurgents. Three years later, Imroz was driving home from court when he felt a cold draught grip his chest. "I slumped over the wheel, inexplicably," he recalled. Bystanders who came to his rescue told him he had been shot. A militant group later claimed it was a case of mistaken identity. In 1996, the Indian army abducted Imroz's friend and fellow lawyer, Jalil Andrabi, whose mutilated body was found after three weeks. Imroz shut himself off. For years he refused to marry or have children, worried they would be targeted. In 2002, his accomplished protégé, Khurram Parvez, a young Kashmiri graduate, was badly injured in an IED attack that killed his driver and a female colleague, Asiya Jeelani. Two years after that, a gunman posing as a client, shot dead another of Imroz's legal allies. In 2005, when Imroz was awarded the Ludovic-Trarieux International Human Rights Prize, first given to Nelson Mandela, he was unable to accept it in person as India declined to issue him a passport.

But Imroz's reputation began to build in the countryside, from where terrified villagers travelled to besiege his rickety chambers on the Bund, in central Srinagar, carrying with them stories. In 2008, these accounts enabled the lawyer to make his greatest discovery. While surveying disappearance cases in villages across two of Kashmir's 23 districts, including Baramulla, from where the three Nadihal men would vanish in 2010, villagers showed him a hitherto unknown network of unmarked and mass graves: muddy pits and mossy mounds, pock-marking pine forests and orchards. According to eyewitnesses, all had been dug under the gaze of the Indian security forces and all contained the bodies of local men. Some were fresh, others decayed, hinting at a covert slaughter that went back many years.

Imroz widened his search, mapping almost 1,000 locations. He was shocked by the implications. Indian law requires that the police probe every violent death and that corpses be identified. But in the village of Bimyar, white-haired Atta Muhammad Khan came forward to describe how he had been forced to inter 203 unidentified bodies under cover of the night – men whose identities and crimes were unstated. "Some corpses were disfigured. Others were burnt. We did not ask questions." It was a similar story in Kichama village, where the lawyer mapped 235 unmarked graves and in Bijhama, where 200 more unidentified corpses had been interred. In Srinagar, Imroz's team alerted the government's State Human Rights Commission (SHRC). "We suspected the missing of Kashmir were buried at these secret sites," he said, publishing a report, Facts Under Ground.

An official response came two months later, just after 10pm on 30 June, 2008. Imroz had at last married Rukhsana, a business woman, and they now had two children, his daughter Zeenish, 12, and a boy, Tauqir, aged seven. The family lived in Kralpora, a tree-lined suburb eight miles from Srinagar city centre. No one called round on the offchance. Rukhsana heard a rap at the door and glanced outside to see that their security lights had been smashed. "I knew what this meant," she said, the door knock immediately conjuring memories of murdered friends. Imroz ran to the back of the house and shouted for his brother, Sheikh Mushtaq Ahmad, who lived next door.

As Ahmad emerged with a torch, a shot was fired, narrowly missing his son. A stranger screamed: "Put that light out." Then, a grenade exploded, shrapnel pitting the front door. Tear gas shells followed, waking neighbours who unlocked the village mosque. The imam mobilised residents to surround Imroz's house, as an armoured vehicle and two jeeps from the paramilitary Central Reserve Police Force and police Special Task Force, took off. "They had come to kill us," Rukhsana recalled. "We need protection," she said. Who do you need protection from, I asked her. "From our own government of course. It's jungle law."

After the attack, Human Rights Watch called on India to "protect Parvez Imroz, an award-winning human rights lawyer" and his case was raised in the European parliament. His family pleaded for him to quit. "I was terrified," the lawyer conceded. "I was starting to have horrible dreams. But being silent is a crime."

Imroz and his team redoubled their efforts, spreading their net across 55 villages in three districts, Bandipora, Baramulla and Kupwara. An ad-hoc inquiry run by volunteers and funded by donations saw the number of unmarked and mass graves mapped rise to 2,700. Inside them were 2,943 bodies; 80% of them unidentified. "These were hellish images from a war that no one has ever reported," said Imroz. "We suspected this to be prima-facie evidence of war crimes," he added. "Who are the dead, how did they die, in whose hands and who interred them?"

The SHRC finally agreed to an inquiry. Soon, it had its work cut out. Using RTI laws, the police were forced to concede that they had lodged 2,683 cases for the covertly interred in just three districts. And a new deposition submitted by Imroz's field workers covering two more districts, Rajoori and Poonch, mapped 3,844 more unmarked and mass graves, taking the total number to more than 6,000. There are still another 16 districts yet to be surveyed, leaving Imroz to wonder how many violent deaths and surreptitious burials have been concealed across Kashmir. Finally, last September, the SHRC made an announcement, stating that Imroz's discovery was correct: "There is every possibility that unidentified dead bodies buried in various unmarked graves … may contain the victims of enforced disappearances." The UN weighed in this year, a report to the Human Rights Council warning India of its obligations under human rights treaties and laws. Kashmiri families had a "right to know the truth" and that "when the disappeared person is found to be dead, the right … to have the remains of their loved one returned to them, and to dispose of those remains according to their own tradition, religion or culture".

After the Nadihal men disappeared, Imroz's field worker, Parvaiz Matta, travelled to the village. He found an eyewitness, Fayaz Wani, a close friend of the missing men. Wani finally revealed the Indian army had offered the men jobs, in a deal brokered by a Special Police Officer (SPO), who had given them a sum equivalent to £7 each, "as a show of good will", before taking them to a remote army camp in Machil.

The families of the missing men filed a complaint against the SPO, Bashir Lone. "This man broke down, admitting his role, claiming that nine soldiers at a remote army camp had shot the three men, so they could claim reward money," Matta said. (The army routinely gives financial rewards to soldiers who kill militants.) On 28 May, 2010, three bodies were exhumed from unmarked graves close to the camp, some of those already mapped by Imroz, and in which the government said were foreign fighters. Their families identified Shahzad, Riyaz and Mohammad by their clothes.

The Nadihal cash-for-killing story and news of a legion of unidentified dead lying in unmarked graves, sent hundreds of thousands of demonstrators on to the streets in the summer of 2010. Sensing the building anger, the army and central government in New Delhi promised an inquiry, offering, without irony, talks to anyone in Kashmir "who renounced violence". However, when no answers came, Kashmir went into convulsions, as crowds of youths armed with stones ambushed soldiers, police and paramilitaries who returned fire with live rounds. I arrived in Kashmir shortly after. More than 100 demonstrators had been killed, many of them children. International news channels briefly took an interest, asking if Kashmir was experiencing its own Arab Spring. But the cameras left quickly, as a vicious crackdown began clearing the streets: the government's own statistics showing that more than 5,300 Kashmiri youths, many of them children, were arrested.

In 2011, Imroz went to work again, investigating how India had restored the peace, and I shadowed him. He took statements from those who had been released and the families of those still incarcerated. "The affidavits made for chilling reading," he said. The majority of youths alleged torture, with independent medical examinations confirming that many had their fingernails pulled and bones crushed. One teenage prisoner told the Guardian: "The police started on our hands and fingers, breaking them with gun butts, and by the end when tears were streaming down our faces, we were hung by our ankles and had chilli rubbed in our wounds." Others claimed to have petrol funnelled into their rectums. One group alleged in court that they were forced to sodomise each other, while a police cameraman filmed.

This year, Imroz and his field workers widened the research to commence the first state-wide inquiry into the use of torture. Their findings will go to the UN and to Human Rights Watch later this summer but a draft seen by the Guardian suggests that not only is torture endemic, it is systemic. In one cluster of 50 villages, more than 2,000 extreme cases of torture were documented, any of which would kick-start an SHRC inquiry, and all of which left victims maimed and psychologically scarred. Methods included branding, electric shocks, simulated drowning, striping flesh with razor blades and piping petrol into anuses.

This work suggests that the statewide ratio for Kashmiris who have experienced torture is one in six. "For the 50 villages, in this small snapshot, we located 50 centres run by the army and paramilitaries in which torture had been practised," Imroz said. The methods, language and even the architecture of the torture chambers are identical. "What we are looking at is not a few errant officers." Files released under RTI laws show how these practises go back to 1989. These documents, seen by the Guardian, also reveal horrific practises, including one sizeable cluster, confidentially probed by the government itself, where men from the Border Security Force (BSF) lopped off the limbs of suspects and fed prisoners with their own flesh.

The Guardian traced one of the victims, a shepherd Qalandar Khatana, 45. Hobbling on crutches, bandages covering his ankles, both feet having been sawn off, he recalled: "I was held down, a BSF trooper produced a knife and then I passed out as the blood gushed from me." His file says a government investigator confirmed the story and produced eyewitnesses.

Another villager, Nasir Sheikh, a carpenter, who lost both legs below the knee and one hand, added: "The smell was of death – urine, shit, sweat. You knew you were about to be slowly murdered. It was like being thrown down a well where no one can hear you scream." His file confirms the story and suggests that compensation be paid. The UN special rapporteur on torture has been refused entry to Kashmir since 1993. Domestic legislation to outlaw torture has stalled. "When will the world start asking as tough questions of India as it is of Syria?" Imroz asked. "Or are we Kashmiris invisible?"

• Kashmir's Torture Trail, Tuesday 10 July at 11:10pm on Channel 4