Every time there is a chance for the United States to escape from the trap it has created for itself in Guantanamo Bay, it slams the door shut.

The Pentagon's decision this week to seek the death penalty for six men it accuses of the 9/11 attacks, and to try them under the hugely disputed version of military courts that it has devised, is one of the stupidest mistakes that the Bush Administration has made.

Everything about Guantanamo is an affront to the values the US says it is defending in the War on Terror. The principle of holding hundreds of people there without charge, for years; the fluid rules of the "military commissions" used for the very few who will be tried; the torture that the Administration acknowledges has been practised on these six: all these are an assault on the US Constitution.

To see the most powerful country in the world scrabbling on the edge of a nearby island, with whose leader it is not on speaking terms, for the sole purpose of evading its own laws and principles, is an embarrassment.

But the pity is that, in charging these six men, the US should have the world on its side. On September 11, 2001, it had the world's appalled, instinctive sympathy. It could have retained that by trying the suspected architects of the assault in its established courts, under principles of justice that go back to its founders.

Instead, it has put itself in an indefensible position by subjecting its captives to new courts, under unclear rules. The Guantanamo trials, already the world's slowest legal process, will implode under waves of justifiable legal challenge, and the world will regard the US, not the 9/11 suspects, as in the dock.

I spent a week in Guantanamo in April 2006, when the pre-trial hearings of the first ten to be charged began. We had seen four years of pictures of men in orange jumpsuits but this was the first chance to hear them speak. The predicament that the US had created for itself was evident from the start.

Every detail of the courtroom was military; the seals of the five services hung on the wall; the judge, or "presiding officer", was a navy captain; the prosecutor was from the Air Force; the defence team from the Army; all were in dress uniform. But in this environment of perfect control - even the metal spiral bindings were removed from notebooks, in defence against God knows what imagined threat - the legal proceedings were chaos.

Two prisoners promptly sacked their Pentagon-appointed lawyers, saying they rejected the court's legitimacy. The judge ordered the defence lawyers, who were also military, to continue; they said that they should put their client's wishes above his orders. The court adjourned while the state Bar associations ruled on whether the defence lawyers could defy a senior military officer; they began (very slowly) giving back different answers, as the 50 states are prone to do. Other lawyers leapt up from the audience to offer to defend the defence lawyers, should they be court martialled. The prisoners, on their first outing from the cells in four years, looked stunned.

These problems have been brewing since the first captives arrived in January 2002 at Guantanamo, the deep bay on Cuba's southern flank that the US claims the right to use under an historic lease. For four years, although the US shipped in more than 700 prisoners, it held no one of more significance than Osama bin Laden's driver.

The Administration lost a Supreme Court case in 2004, on behalf of those detained without charge, and had to drop its claim that the base was not US territory and was outside US law. In the 2006 Military Commissions Act, it watered down two contentious aspects of the trials that had brought fierce criticism from Britain: that suspects could not hear evidence against them, if it was deemed classified; and that evidence obtained from torture could be admitted. US diplomats developed a good line in claiming that if only other countries would take these unpleasant men, then it would shut the base down in a flash, which glossed over the lack of ways for prisoners to challenge their captivity.

But the stakes rose in September 2006, when the US flew in 14 "high-value" prisoners, including Khalid Sheikh Mohammed, the alleged mastermind of 9/11, seized in one of the sporadic moments of co-operation with Pakistan. It acknowledged that the 14 had been held in the CIA's "black prisons" in secret locations abroad, its first admission that these existed.

This week, when the Pentagon declared charges against six, including Khalid Mohammed, it ensured that a blow-torch of attention was directed at the unresolved failings, heightened by its vow to seek the death penalty, that old rift with European allies.

Defence lawyers have had no time to gather evidence. Defendents' rights to challenge evidence or to call witnesses are still unclear. Most troubling, the prosecution plans to get around the objection that the men have been tortured by arguing that the CIA interviews have been repeated without torture by the FBI, who used time-tested rapport-building techniques, officials said, including giving the men Starbucks coffee.

This is indefensible. From the start the US should have tried its captives in its established criminal or military courts. Those it could not charge it should have released. It would have had the world's respect, as well as sympathy. But in setting aside its own principles so easily, it has done profound damage to its standing.

Bronwen Maddox is chief foreign commentator of The Times

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