President Bush has acknowledged the existence of secret CIA prisons and said 14 key terrorist suspects have now been sent to Guantanamo Bay, Cuba.
Bush's policy on terror suspect detainees has been criticised
The suspects, who include the alleged mastermind of the 9/11 attacks Khalid Sheikh Mohammed, have now been moved out of CIA custody and will face trial.
Mr Bush said the prisons were a vital tool in the war on terror and that intelligence gathered had saved lives.
He added that the CIA treated detainees humanely and did not use torture.
He said all suspects would be afforded protection under the Geneva Conventions.
In a televised address alongside families of those killed in the 11 September 2001 attacks, Mr Bush said there were now no terrorist suspects under the CIA programme.
Khalid Sheikh Mohammed (above left): Alleged mastermind of 9/11; believed to be the Number 3 al-Qaeda leader before he was captured in Pakistan in 2003
Abu Zubaydah: Alleged link between Osama Bin Laden and many al-Qaeda cells before his capture in Pakistan in 2002
Ramzi Binalshibh (above right): One of the alleged masterminds of 9/11
Hambali (Riduan Isamuddin): Alleged senior leader in Jemaah Islamiah (JI); wanted by Indonesia, Malaysia, Singapore and the Philippines in connection with blasts
Mr Bush said he was making a limited disclosure of the CIA programme because interrogation of the men it held was now complete and because a US Supreme Court decision had stopped the use of military commissions for trials.
He said the CIA programme had interrogated a small number of key figures suspected of involvement in 9/11, the attack on the USS Cole in 2000 in Yemen and the 1998 attacks on US embassies in Kenya and Tanzania.
Mr Bush spelled out how the questioning of detainee Abu Zubaydah had led to the capture of Ramzi Binalshibh, which in turn led to the detention of Khalid Sheikh Mohammed.
Mr Bush said the CIA had used an "alternative set of procedures", agreed with the justice department, once suspects had stopped talking.
But he said: "The US does not torture. I have not authorised it and I will not."
He said the questioning methods had prevented attacks inside the US and saved US lives.
"This programme has helped us to take potential mass murderers off the streets before they have a chance to kill," the president said.
The CIA programme had caused some friction with European allies. Some EU lawmakers said the CIA carried out clandestine flights to transport terror suspects.
Dick Marty, who investigated the issue of secret CIA prisons for the Council of Europe, said it was now up to European governments to reveal what they know about secret CIA prisons in Europe.
Mr Bush said he was asking Congress to authorise military commissions and once that was done "the men our intelligence officials believe orchestrated the deaths of nearly 3,000 Americans on September 11 2001 can face justice".
All suspects will now be treated under new guidelines issued by the Pentagon on Wednesday, which bring all military detainees under the protection of the Geneva Convention.
All detainees will now have Geneva Convention protection
The move marks a reversal in policy for the Pentagon, which previously argued that many detainees were unlawful combatants who did not qualify for such protections.
The new guidelines forbid all torture, the use of dogs to intimidate prisoners, water boarding - the practice of submerging prisoners in water - any kind of sexual humiliation, and many other interrogation techniques.
The BBC's Adam Brookes in Washington says that in one stroke the Pentagon is moving to defuse all criticism of the way it treats the people it has captured in its war against terrorism.
The US administration has faced criticism from legal experts and human rights activists over the policy on detentions of terrorism suspects.
Mr Bush also said he was asking Congress to pass urgent legislation to clarify the terms under which those fighting the war on terror could operate.
He said the laws must make it explicit that US personnel were fulfilling their obligations under the Geneva Convention.
Mr Bush said those questioning suspected terrorists must be able to use everything under the law to save US lives.