On his second full day in office, President Obama signed an executive order to set right an almost universally acknowledged wrong of the Bush era.

His promise to close the prison camp for terror suspects at Guantánamo Bay within a year was greeted with unconfined joy from all those human rights lawyers and European politicians who have for so long collectively denounced the camp as a scar on America’s conscience.

A book like Guantánamo Boy by Anna Perera, which has crept towards the top of Britain’s bestseller lists, can leave readers with the impression that all the inmates are teenaged, tortured innocents. Mr Obama’s greatest problem in meeting his January 2010 deadline for closing Guantánamo is that this is not true.

Some have undoubtedly been badly mistreated, a few were very young when they were seized, others are guilty of little more than being in the wrong place at the wrong time. But many of the remaining 250 prisoners are hardened al-Qaeda operatives, including Khalid Sheikh Mohammed, the confessed mastermind of the 9/11 attacks.

The Obama Administration says it wants to put most of this group on trial on the US mainland, although exactly how — and how many will face charges — is unclear. It could be through the federal criminal system, military tribunals or some specially constituted national security court. Estimates of the numbers involved range from 20 to 80.

Teams of government lawyers are sorting through often flawed case histories, trying to decide exactly what evidence would be admissible in courts that take a dim view of coercion, let alone torture — as well as how much protection should be given to the intelligence operatives involved in the interrogations.

Legislation may be needed, an inevitably lengthy process, and other controversies are breaking out over where to place prisoners. Talk of upgrading military prisons at Fort Leavenworth, Kansas, or Charleston, South Carolina, has been met with implacable nimbyism from local politicians.

Nor is it proving any easier to deal with the rest of those left in Guantánamo. Although possibly connected to the Taleban or al-Qaeda, these are largely people judged not be a direct security threat to the United States or against whom it has been impossible to assemble a justifiable case.

The Bush Administration wanted to send them back to their home countries, or at least find alternative homes away from the US mainland. So does Mr Obama — but the problems that haunted his predecessor have not disappeared.

Many detainees are from Yemen, a country which has recently released 170 al-Qaeda suspects after receiving promises that they had renounced terrorism. The Americans are uneasy about giving its own detainees a similar “get out of jail free” pass.

More than a fifth of those remaining in the camp are Chinese, Libyan, Russian, Tunisian or Uzbek nationals who might face persecution or death back home. The US has repeatedly asked European allies to help. Albania has taken in a handful of Uighurs, who are part of an Islamic separatist movement in western China, but other countries are wary of antagonising Beijing.

Although Portugal has said it might take other inmates, and some countries such as France, Spain and Sweden have recently promised to look at the proposition on a case-by-case basis, most EU states have rejected it. David Miliband, the Foreign Secretary, says Britain has done enough by taking nine British nationals, three with residency rights, and is doing its best to get two more including Binyam Mohammed.

A senior US State Department official who has been intimately involved in the Guantánamo controversy said: “There is a lot of back-peddling by European countries. They are being wheeled back by security services who know that most of these people are quite dangerous and by public opinion which regards Guantánamo as a US problem.”

The Pentagon claims that as many as 61 former detainees have returned to terrorism since being released, even though it has been slow to justify this figure since the change of Administration. At the back of Mr Obama’s mind, however, must be a sense that he is being set up for a giant “told you so” by his political opponents.

“If you release the hard-core al-Qaeda terrorists that are held at Guantánamo, I think they go back into the business of trying to kill more Americans and mount further mass-casualty attacks,” said former vice president Dick Cheney recently. “If you turn them loose and they go kill more Americans, who’s responsible for that?”

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