On the evening of 11 April 2003, a pair of RAF CH47 Chinook helicopters swept over Iraq's western desert towards a remote rendezvous point beside Route 10, the highway that begins life on the outskirts of Baghdad before running for mile after mile towards the border with Jordan.

As they approached their destination, the crews assumed they were on an operation that would be uneventful. Two days earlier Saddam Hussein's statue had been toppled after American tanks rolled into the Iraqi capital; three weeks later George Bush would stand in front of a banner saying "mission accomplished".

The helicopter crews had been told that a number of detainees were under armed guard at the side of the highway. They were to pick them up after dark and take them to a prison camp. What followed was far from routine: before the night was out, one man had died on board one of the helicopters, allegedly beaten to death by RAF personnel.

The incident was immediately shrouded in secrecy. When the Guardian heard about it and began to ask questions, the Ministry of Defence responded with an extraordinary degree of obstruction and obfuscation, evading questions not just for days but for weeks and months. The RAF's own police examined the death in an investigation codenamed Operation Raker, but this ended with some of the most salient facts remaining deeply buried. The alleged culprits faced no charges.

Asked where the men were being taken, the MoD had initially indicated that they were en route to a prisoner of war camp, one inspected regularly by the Red Cross.

Later it became clear that this was not correct: they were being transported to an altogether more secret location. The truth about the mission raises some searching questions about the legality of some of the British forces' operations carried out in close co-operation with US allies.

One of the first hints that something untoward had happened aboard one of the RAF Chinooks came six years later when Lieutenant Colonel Nicholas Mercer was giving evidence at the public inquiry into the death of Baha Mousa, the hotel receptionist tortured to death by British troops in September that year.

Mercer, who had been the British army's most senior lawyer in Iraq, told the inquiry that by the time of Mousa's death, several other people had died in UK military custody.

Asked about these mysterious deaths, the Ministry of Defence named one of the deceased as Tanik Mahmud, and said he had "sustained a fatal injury" while travelling aboard an RAF Chinook. Perplexingly, the ministry added that the cause of his death remained unknown.

'Unlawful killing'

Asked how they could be sure he had suffered a fatal injury when the cause of his death was not known, the MoD took five weeks to answer.

Eventually, officials admitted that the RAF had received a complaint – anonymously, they said – that "three RAF Regiment personnel on board the helicopter had kicked, punched or otherwise assaulted Mr Mahmud leading to unlawful killing".

This raised many other questions, which the MoD appeared sometimes reluctant to answer.

One of the few that it answered promptly – within hours – concerned the location to which the prisoners were being taken. They were going to Umm Qasr, the MoD said: this was the town on the Kuwaiti border where British and American forces had constructed a large prisoner-of-war camp, a place that came under the supervision of military lawyers and was inspected regularly by the Red Cross.

More information about the incident was to be found in a number of documents released in Australia under that country's freedom of information laws.

The deceased had been one of 64 men detained at a roadblock set up by a soldiers of the Australian SAS. Working alongside a solitary member of a US airforce unit, the 20 Australians were attempting to capture so-called "high-value targets", former high-ranking members of the deposed regime attempting to flee the country.

Seven days earlier, Saddam had appeared suddenly in the middle of a crowd of cheering supporters, an event that was filmed and broadcast on Iraqi TV, along with a speech he was said to have made in which he exhorted his countrymen to "fight them brothers, hit them day and night". The coalition forces were determined to find him.

Three of the prisoners at the side of the highway were suspected of being officials of Saddam's ruling Ba'ath party. Four were held because they were Iranians and in possession of an enormous sum of cash – more than $600,000 – and a letter offering a bounty for each American killed.

The remainder of the prisoners appear to have fallen under suspicion because they were travelling together on a coach. Some were Iraqis and others were Syrian, and all were to be interrogated about Saddam.

None of the 64 were armed, however, and none were in uniform. A number were middle-aged and at least one was severely disabled. Despite this, the men were to be detained as EPWs, enemy prisoners of war. They were to be loaded into the Chinooks in groups of eight and ferried to the prison camp.

As a result of what might be described as a legal sleight of hand, the men were never recorded as prisoners of the 20 Australians. On paper, at least, the lone American was said to have captured them. This meant that the Australian government could consider itself not to be bound by a Geneva convention clause that obliged it to demand the return of any prisoner it transferred to the US if it became apparent that US forces were not treating them in accordance with the convention.

At this point in the Guardian's inquiries, a report written by the squadron leader commanding the 2nd squadron of the RAF Regiment was leaked.

This document, prepared as part of a brief US field inquiry into the incident, showed that the Australians had bound the prisoners' thumbs together before handing them over.

The RAF Regiment gunners then placed hessian bags over the prisoners' heads as they were being led aboard the Chinooks, despite a ban on hooding imposed on the UK's armed forces more than four decades earlier.

Knelt upon

Each prisoner was forced to lie face down on the floor of the aircraft, and those who "refused to adopt the required position" were forced to the floor and knelt upon.

One man who slipped out of his thumb restraint and flailed his arms around was said to have been "lowered" to the floor and "subdued".

By the time the helicopters had reached their destination, two of the prisoners "were found to be unresponsive", according to the squadron leader, while "there was some commotion at the front of the aircraft" because a third prisoner, a disabled man, had somehow parted company with both his prosthetic legs.

It was a windy night, the sand was being whipped up by the Chinooks' rotor blades, and visibility was down to 1.5 metres. The American troops who received the prisoners say the British appeared to be rushing, anxious to transport them all before dawn.

The two "unresponsive" men were loaded into the back of a Humvee vehicle, face down and on top of each other, while the man with no legs was placed in the front passenger seat.

All three were driven to a "holding facility", where one was declared dead. The bag had been taped so securely over his head that it needed to be cut off.

The US inquiry concluded that "appropriate" methods had been used to subdue the man who died. The RAF made no attempt to contact next of kin to inform them of his death, however. Were it not for the anonymous complaint, this would have been the end of the matter.

The complaint is understood to have been made by a member of the Chinook's crew, unhappy at what he saw happening in the helicopter's cabin as they were flying to the camp. After receiving the complaint, the RAF police moved slowly.

According to the MoD, they waited more than a year after the death before asking an RAF pathologist whether the body should be exhumed and examined. Asked to explain the delay, the MoD said the investigators "did not know Mr Mahmud's place of burial".

Once the location was disclosed by the US military, officials explained, "discussions took place on the feasibility of accessing Mr Mahmud's remains, taking into account serious security concerns and obtaining permission from the local imam". At this point, according to the MoD, the RAF pathologist "indicated that given the climate and the degree of decomposition since the death, it would be extremely difficult to establish cause of death". As a result, no postmortem examination was ever carried out.

This advice surprises one eminent civilian pathologist, who says that only exhumation could reveal the state of decomposition.

Derrick Pounder, professor of forensic medicine at the University of Dundee, who has experience of exhumations and postmortem examinations in the Middle East – including cases of deaths in custody – said: "That advice would be contrary to the advice that any UK forensic scientist would offer to any police in the UK who were investigating an allegation of assault leading to death."

He says an examination of the hard tissue may have revealed evidence of an assault before the prisoner died: ribs, for example, sometimes fracture in a distinctive manner when kicked. Asked whether a copy of the pathologist's advice would be made available, the MoD said no copy could be found in its files. After this advice was received the case was passed to RAF's prosecutors, who advised that there was insufficient evidence to bring any charges. They also concluded that any further investigation was pointless.

Asked why the men had been taken as EPWs, when none were armed and all were wearing civilian clothes, the MoD appeared to be stumped.

"UK forces did not detain these individuals, they transported them," the ministry said. "This is not a question we can answer. This question should be directed to the detaining country."

Eventually, the Guardian obtained a copy of the passport that had been in the dead man's pocket, and the death certificate that had been issued by the US military authorities. The passport showed the dead man was a Baghdad odd-job man aged 36. It also showed that his name was not Tanik Mahmud, but Tariq Sabri al-Fahdawi. The RAF police investigation appeared to have been so superficial that it had failed to establish the dead man's identity.

Unknown cause of death

The certificate recorded Sabri's cause of death as unknown. It also showed that the whereabouts of his grave, far from being uncertain, could be pinpointed precisely. The American officer who completed the certificate had gone to considerable lengths to ensure it could be found, beyond the airfield perimeter: "700m out front gate to first culvert, 191 degrees for 50m, next to grave with stacked stones in same location ..."

But of greater significance was what the death certificate revealed about the location of the airfield. It showed that the 64 prisoners had not been flown to the prison camp at Umm Qasr at all. They had been taken an airfield codenamed H1, described on the certificate as the forward operating base of a US special forces unit known as Task Force-20. H1 was an airfield built next to an oil pipeline pumping station.

It was 350 miles north-west of Umm Qasr, in the middle of Iraq's western desert, a vast and desolate expanse of sand and scree. The nearest settlement was many miles away: it is difficult to see how there could have been a "local imam" whose permission needed to be sought before exhumation, or how anyone in the vicinity who could pose "serious security concerns".

The holding facility at H1 was not inspected by the Red Cross. Moreover, its existence was not disclosed to Lieutenant Colonel Mercer, the UK's most senior army lawyer in Iraq at the time. Mercer says he was "extremely surprised" to learn of its existence.

He said: "This matter potentially raises very serious questions. Strenuous efforts were made at all times to ensure that all prisoners were accorded the full protection of the Geneva conventions and vigorous objections would have been raised if there was the slightest possibility of a breach of the conventions. It appears from the information disclosed that some prisoner operations were being conducted, deliberately or otherwise, outside of the chain of command."

The holding facility appears effectively to have been a secret prison – a so-called black site. It is entirely possible, according to international law experts, that taking prisoners to H1 could amount to "unlawful deportation or transfer or unlawful confinement", and that the prisoners were subjected to "enforced disappearances", both of which are war crimes under the Rome statute of the international criminal court.

One former RAF Regiment trooper who was based at H1 for several months has described being involved in a number of similar missions in which prisoners were collected from coalition special forces. This always happened "under total darkness", he says. On arrival at H1, the prisoners were handed on to people whom he describes as "other authorities".

Could this explain why the police investigation into the alleged killing of Tariq Sabri ended with some of the most basic facts – such as his name and the the cause of his death – remaining unknown?

According one well-placed source with knowledge of Operation Raker, the RAF police investigation into the death, there were some at the MoD who were concerned about the possible consequences of a more thorough inquiry: people who were filled with dread at the thought that it could lead to accusations that British forces and others had been involved in crimes against humanity.

When the MoD realised that the location to which the prisoners were flown was known to the Guardian, it quickly apologised for previously stating that they had been flown to Umm Qasr. This had been an innocent mistake, one that a spokesman said could be attributed to "admin/human error".

At this point the MoD also released a copy of the US field inquiry report, which had been withheld from the Guardian for more than a year.

The report showed that a British special forces unit known as Task Force 14, and an Australian unit known as Task Force 64 were an integral part of operations at H1. Both units were under US tactical control.

The ministry also volunteered an admission that the investigation into Sabri's death was not conducted quickly enough. But it said that this could not happen today as its procedures had changed, and added that Operation Raker was now the subject of a review by a team of military police and former civilian detectives known as IHAT – the Iraq historic allegations team.

Asked whether there was any truth in the suggestion that officials had interfered with the investigation into Sabri's death in order to suppress information about the UK's involvement with H1, the MoD replied that IHAT was "giving consideration to any involvement with the investigation of MoD officials who were external to it", and that it would be "inappropriate to comment" while that review was continuing.

Geneva convention

The MoD was also asked whether it was satisfied that UK forces serving at H1 had never been in breach of the Geneva convention, or any other international humanitarian law. It replied by stating only that IHAT would consider the actions of those who came into contact with Sabri.

Nor would the MoD comment on another claim made by the source with knowledge of Operation Raker: that both CIA and MI6 officers were involved in the interrogation of prisoners flown secretly to H1, and that these were the "other authorities" whom RAF Regiment troopers were told would be taking possession of their prisoners. The ministry's only response to questions about non-military interrogators at H1 was a terse: "No further information."

The involvement of the CIA in Task Force 20 is no secret in the US, where it has been disclosed in Pentagon statements and congressional testimony. According to Human Rights Watch, the inter-agency unit was responsible for "some of the most serious allegations of detainee abuse" following the invasion.

Before the end of that year, the unit merged with a similar unit previously based in Afghanistan and changed its name to Task Force 121. By then, however, some at the Pentagon were sufficiently concerned about its methods to send a special investigator to Iraq. Stuart Herrington, a retired military intelligence colonel, discovered that the unit was holding undeclared "ghost" detainees and operating a secret interrogation centre to conceal its activities. Some of its prisoners showed signs of having been beaten.

This was several months before the abuses at Abu Ghraib became known, and Herrington's top-secret report shocked some in Washington. Eventually, somebody leaked it.

Over the years that followed, the unit changed its name again, to Task Force 6-26, and later to Task Force 145, possibly in an attempt to confuse adversaries. Its precise size and the names of its commanders have never been disclosed. But its methods appear to have remained the same. The American Civil Liberties Union obtained a series of US defence documents that showed that the unit's personnel had been investigated repeatedly over their alleged involvement in a catalogue of abuses. In one case, taskforce interrogators were said to have forced a 73-year-old woman to crawl around a room while a man sat on her back, before forcing a broom handle into her anus. Two of her fingers were broken. The woman, a retired teacher, said her interrogators demanded to know the whereabouts of her son and husband, both of whom she said were dead.

In 2006, an investigation by the New York Times found that some taskforce prisoners had been water-boarded, and others were beaten or shot with paintball guns. While a number of interrogators had been prosecuted, posters around one of their bases proclaimed "no blood, no foul": they would be safe as long as none of their subjects bled. The ultimate destination for some of the prisoners who passed though this base was said to be Abu Ghraib. The newspaper's investigation did not uncover the continuing UK involvement with the taskforce, however.

But this became clear when one British member spoke out after quitting the army in disgust. Ben Griffin, a young SAS trooper, said the unit was capturing hundreds of people who were being rendered to prisons where they faced torture, and that he had witnessed dozens of illegal acts by US troops. "My commanding officer at the time expressed his concern to the whole squadron that we were becoming the secret police of Baghdad," Griffin said. The MoD responded by obtaining a court injunction to silence Griffin, and warned he faced jail if he said any more.

The review of Operation Raker being conducted by IHAT is nearing completion, and a report is expected to be handed to the head of the RAF police at the end of this month. The MoD says it is not going to be published.