Khalid Sheikh Mohammed was captured in Pakistan in 2003
US Secretary of Homeland Security Michael Chertoff has promised a fair trial for Guantanamo prisoners accused of organising the 9/11 attacks in 2001.
He was speaking to the BBC after six men, including alleged plot mastermind Khalid Sheikh Mohammed, were charged.
They could face the death penalty if convicted of murder and conspiracy by controversial military tribunals.
But human rights groups have questioned whether such trials can be fair and said the defendants were tortured.
The BBC's Vincent Dowd in Washington says a confession gained from Khalid Sheikh Mohammed may prove problematic as the CIA admitted using "water-boarding" - or simulated drowning - as an interrogation technique.
The London-based group Amnesty International said ill treatment of prisoners was "just one flaw of a commission system set up precisely to obtain convictions under lower standards than would apply in normal courts".
Human Rights Watch, a New York-based organisation, also said the system lacked credibility.
"Possibly putting someone to death based on evidence obtained through water-boarding, or after prolonged periods of sleep deprivation while being forced into painful stress positions, is not the answer," said Jennifer Daskal, a lawyer for Human Rights Watch.
The charges are the first for Guantanamo inmates directly related to the 9/11 attacks.
Mr Chertoff told the BBC that there would be "full due-process and defence lawyers and all of the fundamental rights that would bring to justice those were responsible for one of the worst war-crimes in world history".
Asked if evidence obtained from water-boarding would be used, he said: "The judges will decide what's reasonably admissible."
The Guantanamo Bay detention centre, in south-east Cuba, began to receive US military prisoners in January 2002.
Hundreds have been released without charge but about 275 remain and the US hopes to try about 80.
Brig Gen Thomas Hartmann, a legal adviser to the head of the Pentagon's Office of Military Commissions, said the trials would be "as completely open as possible".
The other five defendants are Ramzi Binalshibh, a Yemeni, Walid Bin Attash, also from Yemen, Ali Abd al-Aziz Ali, who was born in Balochistan, Pakistan, and raised in Kuwait, Mustafa Ahmad al-Hawsawi, a Saudi, and Mohammed al-Qahtani.
Gen Hartmann said the charges included conspiracy, murder in violation of the laws of war, attacking civilians, destruction of property and terrorism.
All but Mr Qahtani and Mr Hawsawi are also charged with hijacking or hazarding an aircraft.
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The charges listed "169 overt acts allegedly committed by the defendants in furtherance of the September 11 events".
Gen Hartmann said the defendants would be given military and civilian defence lawyers and would have the right of appeal.
Khalid Sheikh Mohammed, born in Kuwait of Pakistani extraction, was said to have been al-Qaeda's third in command when he was captured in Pakistan in March 2003.
He has reportedly admitted to decapitating kidnapped US journalist Daniel Pearl in 2002, but these charges do not relate to that.
Conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, intentionally causing serious bodily injury, destruction of property in violation of the law of war, terrorism and providing material support for terrorism (all six defendants)
Hijacking or hazarding a vessel (four defendants only - Ramzi Binalshibh, Walid Bin Attash, Ali Abd al-Aziz Ali and Khalid Sheikh Mohammed)
The charges will now be sent to Susan Crawford, the convening authority for the military commissions, to determine whether they will be referred to trial.
Any trials would be held by military tribunal under the terms of the Military Commissions Act, passed by the US Congress in 2006.
The act set up tribunals to try terror suspects who were not US citizens.
The law is being challenged by two prisoners at Guantanamo Bay, who say they are being deprived of their rights to have their cases heard by a US civilian court.
Responding to the new charges, a representative of Mohammed al-Qahtani said they would create "show trials".
Nineteen men hijacked four planes in the 9/11 attacks. Two planes hit the World Trade Center in New York, another the Pentagon in Washington and the fourth crashed in Pennsylvania.
Zacarias Moussaoui, a Frenchman of Moroccan descent, is the only person to have been convicted in the US in relation to 9/11. In 2005, he was sentenced to life in prison for his role in planning the attacks.