Baghdad's Medical Forensic Institute - the mortuary - is a low, modern building reached via a narrow street. Most days it is filled with families of the dead. They come here for two reasons. One group, animated and noisy in grief, comes to collect its dead. The other, however, returns day after day to poke through the new cargoes of corpses ferried in by ambulance, looking for a face or clothes they might recognise. They are the relatives and friends of the 'disappeared', searching for their men.

And when the disappeared are finally found, on the streets or in the city's massive rubbish dumps, or in the river, their bodies bear the all-too-telling signs of a savage beating, often with electrical cables, followed by the inevitable bullet to the head.

In a new twist in the ongoing brutality of this country, Iraqi-on-Iraqi violence is escalating dramatically.

Last July an Observer investigation reported that Iraqi police commandos were running secret torture units, and last week there was international outrage when an Iraqi government bunker was found being used as a makeshift prison. American forces found 173 half-starved prisoners being held in dreadful conditions. Most were Sunnis.

The new trend in violence is one that Dr Alaa Maki of the Iraqi Islamic Party is familiar with. A month ago his bodyguard, Alaa al-Azawi, was taken from his home with his two brothers by police at midnight. The family were told the men were being taken for investigation. The following day his body was dumped in the street.

Eight days ago, another of Maki's friends was being treated in the Yarmouk Hospital, Iraq's second- biggest, in the western suburbs of Baghdad. His relatives, Muamir Saad Mahmoud and Ali Mahmoud, went to visit him. Instead they met men in the uniform of Iraq's police waiting for them.

Ali was later released in the vast Shia slum of Sadr City after a violent beating. Muamir has not been seen. Dr Maki and the family are now waiting for his body to turn up.

And it is not just in Baghdad. The home of Khalid Ahmad Harbood, a resident of the Alkadisia neighbourhood of Madain city, was raided at midnight on 13 October by the Alkarrar brigade, commandos of the Ministry of the Interior. Harbood was detained at their base. Transferred to the 'Panorama building' in the town, he was tortured so badly over the period of a week that he died and his badly battered body was dumped in Sadr City.

As is so often the case in Iraq these days, the details are difficult to corroborate, but they fit a pattern.

According to human rights organisations in Baghdad, 'disappearances' - for long a feature of Iraq's dirty war - have reached epidemic proportions in recent months. Human rights workers, international and local, who asked not to be identified in order to protect their researchers in the city and their organisations' access to senior government officials, told The Observer last week that they have hundreds of cases on their books. They described the disappearances as the most pressing human rights issue in a country that is in the midst of a human rights disaster.

The crisis was underlined by last week's uncovering of the secret Ministry of the Interior detention facility in the well-to-do neighbourhood of Jadriya.

It led the US embassy in Baghdad to forcefully condemn the new Iraq's culture of torture and killing - a statement that many believe has been too long in coming.

The emergence of a culture of pernicious violence at Iraq's interior ministry blossomed in the face of repeated warnings to US and UK officials over the past year and a half, under an apparently deliberate policy by London and Washington to avoid public criticism of the country's new institutions.

It is a silence that persisted despite compelling evidence provided by human rights organisations, journalists and Iraqi officials that, from the very moment of the hand-over of sovereignty, violent abuses were being committed in the Ministry of the Interior building - the results of which have been witnessed by The Observer

Then, as in last week's discovery of the starving prisoners, the abuses were only uncovered during a raid by American military police who had been tipped off that prisoners were being beaten in a 'guesthouse' in the ministry's grounds.

It was, in retrospect, the beginning of a pattern of behaviour that would only worsen as the months went by. The Observer has gathered a catalogue of mistreatment by the elements of the very police forces that Washington and London have been counting on as the front line in the fight against insurgents and terrorists.

Among those to be confronted early in the interim government with the way in which policing in Iraq was going was a senior British police officer, involved in mentoring the new Iraqi Police Force, who described to this paper how he had entered the room of a deputy minister and found a man with a bag over his head standing in the corner.

In retrospect, it would turn out to be a minor abuse in comparison with what would follow. Instead, the roots of the human rights catastrophe that has enveloped the ministry were to be found in the simmering sectarian conflict of tit-for-tat assassinations that had taken hold in Baghdad's vast suburbs.

There, the armed militia of the Supreme Council for the Islamic Revolution in Iraq, the Badr Brigades, had begun a campaign of revenge attacks against former members of the largely Sunni secret police, the mukhabarat, tactics that would be imported wholesale into the Ministry of the Interior when SCIRI - and the Badrists - took control of it after the elections.

By the early months of this year, a militia widely accused by Sunnis of a campaign of assassination had become integrated into the newly emergent Special Police Commandos under the command of the ministry, led by a senior member of the Supreme Council for the Islamic Revolution in Iraq, Bayan Jabr. The Badr Brigade's campaign would become integrated into one of the Iraqi government's most powerful ministries.

'The origins of what is going on now go back to the period from April to May 2003,' said a British security source. Then members of the Badr Brigades returning from exile in Iran began a vendetta against Baathists, largely former members of the mukhabarat. It is a campaign that has widened as it has continued and what is worrying now is the extent to which it is tacitly sanctioned.

By the spring and early summer of this year worrying reports were beginning to emerge of secret interrogation facilities where torture and extrajudicial killings were taking place at sites directly controlled by the Ministry of the Interior or associated with police commando units under its command; a list of alleged sites was published by The Observer. Even then, with the accusations of abuse fully in the open, and with the Foreign Office admitting it had privately relayed its concern about the abuses to the Iraqi government, the policy of the US and the UK was to keep up pressure behind the scenes.

Pressure was also brought to bear by Unami, the UN Assistance Mission to Iraq, a joint effort that, by August at least, seemed to have brought some success when Interior Minister Bayan Jabr circulated an order reminding police that they must respect the rights of detainees. It would mark the beginning of an ever more violent and secretive campaign that would see disappearances in the Baghdad area escalate beyond anything that had been witnessed before. And it is taking a sinister new form.

At 9pm on 25 September a Toyota pick-up truck without number plates turned up at the house of 'H' - who has asked that neither his name nor the neighbourhood in which he lives in eastern Baghdad be identified for his family's sake. Inside the pick-up were eight men in civilian clothes and black balaclavas, wearing body armour with the word 'Police' stencilled in large letters. They arrested H's son - a man in his mid-twenties - the only Sunni living in a Shia neighbourhood.

'There has been a marked change in what has been going on,' said one senior human rights worker in Baghdad who is involved in monitoring the cases of the disappeared. His organisation has asked not to be identified.

'Between May and August last year we would see people being picked up in what looked like conventional raids by officers in police cars and uniforms, often supported by multinational forces.

'What has been happening since August is that when people are being picked up it is by people out of uniform, but who may turn up in Ministry of the Interior vehicles or show MoI ID cards. Many of those people are turning up with a bullet in the head.'

It is a state of affairs forcefully described in the most recent Unami human rights report released in October, and handed to the Iraqi government. 'It is extremely worrying,' it reported on the issue of sectarian murders, 'that some of these crimes are committed by individuals wearing police and military uniforms and using police or military equipment.'

What is also of deep concern for both human rights officials, as well as Iraqis such as Dr Maki, is the fact that, despite repeated complaints, there appears to have be almost no effort by the government or the Ministry of the Interior to investigate them seriously.

Indeed, last week, despite the powerfully worded complaint by the US ambassador over the latest human rights abuses, Bayan Jabr and his spokesmen continued to deny all knowledge of abuses and murders, attributing it to vague claims of infiltration of the 'ministry and police', and accusing those drawing attention to the abuses of trying to stir sectarian violence.

It is not an answer that has much impressed Human Rights Watch, which has been cataloguing abuses by the Ministry of the Interior for the past year and a half.

'The point that needs to be made again and again,' says Sarah Leah Whitson, an executive director of Human Rights Watch, 'is that saying you do not know is no defence. The fact that the minister does not know is an admission of failure. It is his job to know.'

It is a view echoed by Dr Maki of the Iraqi Islamic Party, which last week called for an international investigation of the human rights abuses by Ministry of the Interior forces following the discovery of the secret detention facility in Jadriya.

'We blame the government for these events, and no matter how often we have complained there has been no investigation. I have spoken to the UN. I have handed over a dossier of what has been going on.

'We have been trying to persuade the US and UK governments for the past two years about what has been going on. It has taken until now to convince them that this is real.'

In the meantime, as the disappearances have escalated in recent months, so whatever small faith Sunnis had in Iraq's judicial process has increasingly collapsed, falling back instead on the tribal code permitting revenge killings.

And so the violence in Iraq continues.