Cover-up: Charles Clarke knew exactly how dangerous released prisoners were. But he kept it secret

It is an interesting question as to when, exactly, Mr Clarke knew that the firestorm over the bungled release of 1,023 foreign prisoners would ignite. Now that it is raging, however, he needs no lessons in how to damp down the flames.

The Home Secretary is this weekend masterminding an operation to round up the 79 most serious offenders. By staging a series of high-profile raids, he hopes to parade those caught on the evening news bulletins, to restore the public's trust.

But even now Mr Clarke is still failing to tell the whole truth about the danger he has placed on Britain's streets. As The Independent on Sunday reveals today, the Home Secretary's statement yesterday that of the 79, 13 had committed the "most serious offences" of "murder, manslaughter, rape and child sexual offences" disguises the true scale of the threat.

A breakdown exclusively obtained by this newspaper shows that the priority list includes four kidnappers, two murderers, eight rapists, 13 sex offenders, two killers convicted of manslaughter and 50 violent offenders.

Although the Home Office knows this information and has passed it on to the Association of Chief Police Officers (Acpo), it has deliberately withheld the breakdown from the public. David Davis, the shadow Home Secretary, condemned what he termed a "cover-up", the latest incidence, he said, of Home Office evasion. "They haven't been straight with the numbers," he said last night. "We've had to drag the numbers out of them."

Mr Clarke belatedly admitted on Friday night that five of the 79 most serious offenders had committed further crimes relating to drugs, violent disorder and grievous and actual bodily harm. A further two are under investigation for sex offences, including rape. Crucially, one of those under investigation was released from prison after Mr Clarke was told about the problem.

It was on Tuesday at lunchtime that Mr Clarke released a letter to Edward Leigh, the chairman of the Public Accounts Committee (PAC), admitting that the Home Office had grossly underestimated the number of foreign prisoners released without deportation being considered. MPs had been asking increasingly difficult questions about the issue and were looking forward to quizzing the top mandarin in charge at the time, Sir John Gieve, on Thursday.

Mr Clarke has tried to present the disclosure ahead of this meeting as proof of his openness on the issue, but the IoS has learnt that right to the end, the Government was trying to frustrate the committee. Sir Gus O'Donnell, the Permanent Secretary, tried to prevent Sir John, now a deputy governor at the Bank of England, from appearing before the PAC on the grounds that only serving civil servants are accountable to Parliament.

After a fierce tussle, the MPs won the day, and on the eve of the meeting Mr Clarke was forced to come clean. By chance, Tony McNulty, the Minister of State for Immigration, was accompanying Tony Blair on a visit to north-west London as the media began to react to the extraordinary news of the foreign prisoners on Tuesday afternoon.

Mr Blair collared the likeable minister as he returned to Downing Street for an in-car briefing on the background to the scandal. It made for a sorry tale.

The political omens do not look promising for the Home Secretary this weekend. Despite repeated expressions of No 10 support, he knows Mr Blair's backing is not infinite. He also knows that he blundered badly on Tuesday night when he told Newsnight that "very few" prisoners had been released after he learned of the issue. In fact, the figure was 288.

According to his friends, he knew straight away he had made a terrible error. "He knew he had screwed up pretty much immediately. It was stupid - the 288 figure had already been released."

First Mr Blair and then Mr Clarke were made to pay heavily for the mistake as the Tory leader, David Cameron, and Mr Davis came close to accusing the Home Secretary of lying.

Mr Clarke's defence of his claim that "very few" had been released was embarrassing to watch, even to his friends. "Perhaps my use of language was infelicitous, but I was thinking of the thousands who were successfully deported over that time and the large number of people whom we are looking at in the round."

The next day, he did not hang around for long in the Commons tea room. The tour of the backbenchers' canteen by a minister on death row can be a risky political ritual to observe. The Home Secretary may have concluded he was getting insufficient support from his colleagues and decided not to outstay his welcome.

Meanwhile, upstairs, the impression that his department was hopelessly out of control was being reinforced as Sir John finally answered a barrage of hostile questions from the PAC. The top mandarin in charge at the time of the release of foreign prisoners eligible for deportation was given a roasting over his time in charge, particularly over his control of the Home Office's accounts.

Richard Bacon, the MP whose questions exposed the scandal, brandished a copy of an internal audit carried out last November into accounts processed on the department's new Adelphi IT system.

The report, an extract of which has been obtained by the IoS, found that, although the books balanced, when the auditors added up the figures they totalled £26 trillion.

This, the report notes dryly, is "almost 2,000 times higher than the Home Office's gross expenditure for 2004-05 and approximately one and a half times higher than the estimated GDP of the entire planet. This suggests that something has gone seriously awry with Adelphi processing during 2004-05. We have yet to receive an explanation for what has happened."

With accounting like that, cynics might suggest, it is perhaps not surprising that the Home Office failed to co-ordinate hundreds of overcrowded prisons and an over-worked Immigration Service. It also raises the question of how many other failures are festering beneath the surface. Mr Clarke, for one, does not discount yet more bad news. In an extraordinary exchange after his Commons statement on Wednesday, he agreed "completely" that the Home Office was a "seriously dysfunctional organisation".

So how were more than 1,000 foreign prisoners eligible for deportation allowed to walk out of jails across the country after serving their sentences without being picked up and sent back to their home countries?

Numerous factors have been blamed for this fiasco, including the soaring number of foreign nationals in British jails, failures by immigration staff to monitor foreign prisoners adequately and an obsession with clearing the backlog of asylum applications at the cost of deportations.

What is clear is that the problems are historic. Ministers were warned there was an "institutional blind spot" on how foreign nationals were dealt with as far back as 2003, with prisons not even knowing how many they held.

The chronic overcrowding in British jails is partly down to the massive rise in foreign nationals being held as a result of a clampdown on drug trafficking. Figures have risen by 152 per cent over the past 10 years, with one in eight now from abroad, including countries such as Jamaica.

A letter to staff sent by Sir David Normington, the Home Office's top civil servant, on the day that the deportation crisis blew up highlights just how overwhelmed immigration staff are by the number of cases they have to deal with.

The memo, a copy of which has been obtained by this newspaper, states: "The foreign national prisoner population is at record levels and it is clear that while an increasing numbers [sic] of cases have been referred for consideration, we have not kept pace with that rising demand."

It goes on: "This is clearly a situation that all of us would rather have avoided, and we must all do our best to ensure that our systems are sufficiently robust to help prevent this kinds of major issue from arising."

The IoS has also learnt that during 2000 to 2004 staff were moved from deportation duties to tackle the asylum backlog, which led to huge delays in the processing of deportation recommendations. On numerous occasions, deportation hearings were adjourned because paperwork was not ready or because inmates were not produced by the Prison Service.

Officials give confusing accounts about how foreign prisoners who are eligible for deportation should be dealt with. Judges normally recommend deportation when an offender is sentenced, and it is assumed that they will leave the country when they have reached the end of their prison term.

In at least 160 cases out of the 1,023, criminals released, but not deported, by the Home Office, judges had made such a recommendation. The Home Office can also make its own independent application for an offender to be deported.

Insiders say they are often unable to take action on prisoners until the end of their sentences because of complaints by prisoners that they are being unjustly targeted.

Prisoners are also not obliged to produce a passport or any other document as proof of identity. Often, their details may be wrong or the prisoner deliberately lies about their true identity or their country of birth. This can lead to confusion within the system.

It would be impossible for individual prisons to hang on to inmates because the Prison Service has a legal duty to release prisoners once they have served their sentences.

Prison sources say they did flag up foreign nationals when they entered prison and near their release dates to the Immigration Service but they often received no response, so were obliged to release them. "The Immigration Service was consistently told again and again that this was an issue but the response was they were too busy dealing with other things," one said.

Despite promises of tough and immediate action by ministers, there are no signs that the chaos over the handling of foreign nationals has abated. One immigration official said that he knew of up to 20 foreign nationals in one prison alone who over the last week had not been reported to the Immigration Service. "People are increasingly realising that if they do not give their full details then they cannot be removed," he said.

Mr Clarke also has to face the possibility that even if all the prisoners who were allowed to slip through the net are picked up, it may take months to deport them. In some cases, it may be impossible to send them back if there is no proof of where they came from.

Senior Whitehall sources say that ministers are trying to work with Austria, which currently has the EU presidency, to draw up an agreement on fast-tracking for deportation EU nationals, who account for a substantial proportion of the current foreign national prison population.

But Harry Fletcher, from the National Association of Probation Officers (Napo), warned that more prisoners would be let out of jail and not sent back unless more cash is made available.

"The immigration and prison services have suffered from years of underfunding and poor management. Unless resources are allocated immediately, more prisoners will be let out and not deported."

John Tincey, from the Immigration Service Union, said the deportation crisis could rumble on for months and that ministers faced huge opposition from judges if they tried to detain released criminals indefinitely. "They can be held in detention centres, but this would be very difficult if they are rapists or child sex offenders. And you can't just put people on a plane because they will bounce back."

Ironically, Mr Clarke's best hope for survival lies with the chance that the focus of media attention will swing away from him and on to another cabinet heavyweight.

Foreign Prisoners: The Zimbabwean rapist who is back behind bars

Kyle Bester is one of 1,023 foreign prisoners released when they should have been deported. A Zimbabwean, he was arrested and charged after attacking a woman in a Guildford nightclub in 2001.

According to the Crown Prosecution Service, the victim had little recollection of the events but experienced "mental flashbacks" of being violently raped.

She reported the incident in the early hours of that morning, but it was nearly two years before police tracked down Bester. He was arrested for a driving offence. The DNA he provided matched a sample obtained from the rape victim.

Following trial at Guildford Crown Court, Bester was convicted and sentenced to five years. After two and half years he was released. He should have been deported but, reportedly, the Home Office lost his papers.

Bester was re-arrested last Friday and taken to Belmarsh top-security prison while he awaits deportation.

But his father, Andre, yesterday said his son was appealing against his rape conviction and had been informed by the Home Office that he could stay in the UK until the case had been heard.

"It all boils down to Charles Clarke and what has been going on in the media lately. They are just looking for a scapegoat," said Mr Bester.