When I first interviewed him a year ago he was suspected of contacts with the insurgency. Certainly he supported resistance to US forces.

More recently, an-Ni'ami had dropped out of sight. Then, a little over a month ago, relatives say, paramilitary police commandos from 'Rapid Intrusion' found him at a family home in the Sha'ab neighbourhood of northern Baghdad. His capture was reported on television as that of a senior 'terrorist commander'. Twelve hours later his body turned up in the morgue.

What happened to him in his 24 hours in captivity was written across his body in chapters of pain, recorded by the camera. There are police-issue handcuffs still attached to one wrist, from which he was hanged long enough to cause his hands and wrists to swell. There are burn marks on his chest, as if someone has placed something very hot near his right nipple and moved it around.

A little lower are a series of horizontal welts, wrapping around his body and breaking the skin as they turn around his chest, as if he had been beaten with something flexible, perhaps a cable. There are other injuries: a broken nose and smaller wounds that look like cigarette burns.

An arm appears to have been broken and one of the higher vertebrae is pushed inwards. There is a cluster of small, neat circular wounds on both sides of his left knee. At some stage an-Ni'ami seems to have been efficiently knee-capped. It was not done with a gun - the exit wounds are identical in size to the entry wounds, which would not happen with a bullet. Instead it appears to have been done with something like a drill.

What actually killed him however were the bullets fired into his chest at close range, probably by someone standing over him as he lay on the ground. The last two hit him in the head.

The gruesome detail is important. Hanging by the arms in cuffs, scorching of the body with something like an iron and knee-capping are claimed to be increasingly prevalent in the new Iraq. Now evidence is emerging that appears to substantiate those claims. Not only Iraqis make the allegations. International officials describe the methods in disgusted but hushed tones, laying them at the door of the increasingly unaccountable forces attached to Iraq's Ministry of the Interior.

The only question that remains is the level of the co-ordination of the abuse: whether Iraq is stumbling towards a policy of institutionalised torture or whether these are incidents carried out by rogue elements.

Six months ago, Human Rights Watch (HRW) laid out a catalogue of alleged abuses being applied to those suspected of terrorism in Iraq and called for an independent complaints body in Iraq.

But as the insurgency has grown hotter, so too, it appears, have been the methods employed in the dirty counter-insurgency war.

To add to HRW's allegations of beatings, electric shocks, arbitrary arrest, forced confessions and detention without trial, The Observer can add its own charges These include the most brutal kinds of torture, with methods resurrected from the time of Saddam; of increasingly widespread extra-judicial executions; and of the existence of a 'ghost' network of detention facilities - in parallel with those officially acknowledged - that exist beyond all accountability to international human rights monitors, NGOs and even human rights officials of the new Iraqi government.

What is most shocking is that it is done under the noses of US and UK officials, some of whom admit that they are aware of the abuses being perpetrated by units who are diverting international funding to their dirty war.

Hassan an-Ni'ami may well have been a terrorist. Or he may have had knowledge of that terrorism. Or he may have been someone who objected too loudly to foreign troops being in Iraq. We will never know. He had no opportunity to defend himself, no lawyer, no trial. His interrogation and killing were a breach of international law.

And it is not only the case of an-Ni'ami but others too, all arrested by units of the Ministry of the Interior, many of whom were tortured and subsequently killed. Post-mortem images show a dozen or so farmers from the insurgent hotbed of Medayeen who were apparently seized by police as they slept in one of Baghdad's markets and whose bodies were discovered on a rubbish dump in shallow graves to the north of the city. Like an-Ni'ami, their bodies also bore the marks of extensive torture before execution, most with a bullet to the head.

The face of the first body is blackened by strangulation or asphyxiation. Another has bruises to his forehead where he was been hit repeatedly with something heavy. Yet another, his hands still tied with cord, has been punched in the eye and had his ankle fractured. Yet another shows signs of burning similar to an-Ni'ami's. The last two have identical puncture wounds, fist-width apart, suggesting the use of a spiked knuckle-duster.

Then there is Tahar Mohammed Suleiman al-Mashhadani, seized from the Abu Ghraib neighbourhood from early prayers outside a mosque with a number of other men, again by paramilitary police from Rapid Intrusion. When his body was found by family members in the morgue - 20 days after his arrest - he had been tortured almost beyond recognition.

These are not isolated cases. For what is extraordinary is the sense of impunity with which the torture, intimidation and murder is taking place. It is not just in Baghdad. In the majority Shia south, far from the worst ravages of the insurgency, there are also emerging reports consistent with the abuses in the capital.

If there is a centre to this horror, it is Baghdad's Ministry of the Interior, and the police commando units that operate from there.

The ministry is a strange, top-heavy building, set apart in an area of open ground off the highway. Its entrance is guarded by concrete blast-walls and endless checkpoints on the dusty road that leads to its crowded reception.

I came here almost exactly a year ago, two days after sovereignty had been handed back to Iraq's interim government. The floors were occupied by civil servants and blue-uniformed officers of the Iraqi Police Service. It was easy to wander in.

These days the ministry is a very different place. The dusty hinterland that leads to it is busy with the new paramilitary forces that most often have been accused of human rights abuses - the Rapid Intrusion brigades, most notoriously the Wolf Brigade of 'Abu Walid'. There has been no investigation or official findings over the allegations.

It was here - 12 months ago - that there was the first intimation that something was going seriously wrong. On the second day of Iraq's new government, US military police were forced to raid the Guest House to 'rescue' dozens of alleged criminals, scooped up in a sweep of the city, who were being subjected to beatings and forced confessions of their crimes.

Back then officials were happy to justify the violence - and angry at the US intervention. Criminals and terrorists expected a good beating, one official said, proud of his 100 per cent confession rate.

Now it is impossible to reach those officials as they shelter on heavily guarded floors. There are no American MPs to come to the aid of those locked in the cells.

A year ago, the worst violence was meted out in the Guest House. Now officials say the abuse happens on the seventh floor, where those suspected of terrorist connections are brought.

One of those held at the ministry for 'terrorist interrogation' is 'Zaid'. It is not his real name. Since his release, the 25-year-old Sunni from the western suburbs of Baghdad lives in fear of being brought back.

A taxi driver, the college graduate stopped his car in March to buy food in a market. When a bomb exploded nearby, he went to look at the damage. Arrested at the scene by soldiers from the Iraqi National Guard, he says he was handed over to the Ministry of the Interior.

At first, said Zaid, he was put in a room, on the seventh floor, measuring 10ft by 12ft, with 60 others. He was crammed in so tightly he could not sit. In some respects Zaid was lucky. Early in his detention, a Ministry of Justice official appeared and, furious at the conditions, demanded the men be moved. 'He said, "You can't have this many people in a room this size," so they moved us to somewhere with more air and fed us. He asked too whether there had been any beatings and some said yes.'

For his part, Zaid says he was hung by his arms, but not for so long that it caused any permanent damage. His ordeal was largely to be subjected to threats of violence as up to eight guards circled him during his interrogation. But Zaid claims he witnessed what happened to men brought from another detention facility, a barracks run by the Wolf Brigade, who were kept in the same area as Zaid until his parents paid a hefty bribe for his release.

'I saw men from Samarra [another insurgent stronghold] and from Medayeen. Some appeared to have wounds to their legs,' he recalled. 'There were others who could not use their spoon properly. They had to hold it between their palms and move their heads to the spoon.'

His month in the ministry terrified Zaid. If the police came again for him, he said, he would rather throw himself off a balcony than go back. Zaid is not the first detainee to accuse the police of taking bribes for the release of prisoners. It is a common charge, as are descriptions of prisoners being brought from other, less accountable, interrogation facilities where the worst of the violence is taking place.

What is most important about Zaid's testimony is that it makes clear a link exists between the Ministry of Interior and the torture being conducted out of sight at other centres. Iraqi and international officials named several of these centres, including al-Hadoud prison in the Kharkh district of Baghdad.

A second torture centre is said to be located in the basement of a clinic in the Shoula district, while the Wolf Brigade is accused of running its own interrogation centre - said to be one of the worst - at its Nissor Square headquarters. Other places where abusive interrogations have been alleged include al-Muthana airbase and the old National Security headquarters.

'Abu Ali', a 30-year-old Sunni scooped up in a mosque raid in central Baghdad, was taken to the latter for a week in mid-May where he says he was beaten on his feet, subjected to hanging by his arms and, when he angered his guards by refusing to confess, threatened with being sat on 'the bottle' - being anally penetrated.

It is not just in Baghdad. Credible reports exist of Arab prisoners in Kirkuk being moved to secret detention facilities in Kurdistan, while other centres are alleged in Samarra, in the Holy Cities and in Basra in the south.

'There are places we can get to and know about,' said one Iraqi official. 'But there are dozens of other places we know about where there is no access at all.'

'It is impossible to keep track of detentions, and what is happening to people when they are taken away,' complained one foreign official involved in trying to building Iraq's respect for human rights.

'On top of that we have a whole culture that is permitting torture. The impression is the judiciary are simply not interested in responding to the issue of human rights. It is depressing.'

But it is not simply the issue of keeping track of where detainees are being taken that is a problem. Accountability has also become more opaque since the formation of the Shia-dominated government of Ibrahim Jaffari with ministers and senior officials at the Ministry of the Interior refusing to meet concerned international organisations including Human Rights Watch.

'We have been trying to break through to someone responsible to express our concerns,' said another international official.

'But it is impossible to meet the people we really need to see. What is so worrying is that allegations concerning the use of drills and irons during torture just keep coming back. And we have seen precisely the same evidence of torture on bodies that have turned up after they have been arrested. There is a dirty counter-insurgency war, led on the anti-insurgency side by groups responsible to different leaders. People are not appearing in court. Instead, what is happening to them is totally arbitrary.'

There is a significance to all this that goes beyond the everyday horror of today's Iraq. In the absence of weapons of mass destruction, the human rights abuses of Saddam Hussein's regime became more important as a subsidiary case for war.

It has been a theme that has been constantly reiterated: it was horrific then, and it is better now. The second may still just be true. In many aspects there may be some improvement, but the trajectory of Iraq now on human rights is in danger of undermining that last plank of justification.

True, there is a question of scale of the abuses. What is also different from Saddam's era is that Iraq is now host to multinational troops, to huge UK and US missions, and is a substantial recipient of foreign aid, including British and EU funds.

British and US police and military officials act as advisers to Iraq's security forces. Foreign troops support Iraqi policing missions. What is extraordinary is that despite the increasingly widespread evidence of torture, governments have remained silent. It is all the more extraordinary on the British side, as embassy officials have been briefed by senior Iraqi officials over the allegations on a number of occasions and individual cases of abuse have been raised with British diplomats.

In Iraq's Ministry of Human Rights, close to the Communications Tower and the location of one of the secret interrogation centres, they were marking the international day for the victims of torture. As officials gathered for chocolate cake and cola under posters that read 'Non to torture', some senior officials are in no doubt that torture in their country is again getting worse.

The deputy minister, Aida Ussayran, is a life-long human rights activist who returned from exile in Britain to take up this post. She concedes that abuses by Iraq's security forces have been getting worse even as her ministry has been trying to re-educate the Iraqi police and army to respect detainee rights.

'As you know, for a long time Iraq was a mass grave for human rights,' she says. 'The challenge is that many people who committed these abuses are still there and there is a culture of abuse in the security forces and police - even the army - that needs to be addressed. I do not have a magic solution, but what I can do is to remind people that this kind of behaviour is what creates terrorists.'

There is a sense of frustration too in the Ministry of Human Rights, for even as the security forces rapidly increase in size, the ministry tasked with checking abuses has only 24 monitors to pursue cases, at a time when officials believe it needs hundreds to keep Iraq's police and army effectively in check.

If Ussayran is robust about her country's problems with human rights abuses, others are convinced that, far from being the acts of rogue units, the abuse is being committed at the behest of the ministry itself - or at least senior officials within it.

'There are people in the ministry who want to use these means,' said one. 'It is in their ideology. It is their strategy. They do not understand anything else. They believe that human rights and the Convention against Torture are stupid.'