Mohammed al-Qahtani was one of six men charged by the military in February with murder and war crimes for their alleged roles in the 2001 attacks. Authorities say al-Qahtani missed out on taking part in the attacks because he was denied entry to the U.S. by an immigration agent.
But in reviewing the case, the convening authority for military commissions, Susan Crawford, decided to dismiss the charges against al-Qahtani and proceed with the arraignment for the other five, said Army Lt. Col. Bryan Broyles, the Saudi's military lawyer.
Crawford dismissed the charges Friday without prejudice, meaning they can be filed again later, but the defense only learned about it Monday, Broyles told The Associated Press.
The attorney said he could not comment on the reasons for the dismissal until discussing the case with lawyers for the other five defendants. Officials previously said al-Qahtani had been subjected to a harsh interrogation authorized by former Defense Secretary Donald H. Rumsfeld.
A Pentagon spokesman, Navy Cmdr. Jeffrey Gordon, confirmed the case was proceeding against the five defendants and that their arraignment will be within 30 days of the charges being served at the U.S. base at Guantanamo Bay, Cuba.
Gordon declined further comment since the Office of Military Commissions had not yet released the formal announcement about the legal developments.
The five defendants include Khalid Sheikh Mohammed, the suspected mastermind of the terrorist attacks in 2001 that killed nearly 3,000 people, and Ramzi Binalshibh, who is said to have been the main intermediary between the hijackers and al Qaeda leaders. Prosecutors are seeking the death penalty for all of them.
Their trial is the first capital case thus far before the military tribunals at Guantanamo, where the U.S. holds about 270 men on suspicion of terrorism or links to al Qaeda and the Taliban. The military has said it plans to prosecute about 80 prisoners in the first U.S. military war crimes tribunals since World War II.
Authorities have said they plan to broadcast the trials to military bases in the United States so relatives of the victims of the attacks can see the proceedings.
Critics of the tribunals have faulted a rule that allows judges to decide whether to allow evidence that may have been obtained with "coercion." U.S. authorities have acknowledged that Mohammed was subjected to waterboarding by CIA interrogators and that al-Qahtani was treated harshly at Guantanamo.
Al-Qahtani last fall recanted a confession he said he made after he was tortured and humiliated at Guantanamo.
The alleged torture, which he detailed in a written statement, included being beaten, restrained for long periods in uncomfortable positions, threatened with dogs, exposed to loud music and freezing temperatures and stripped nude in front of female personnel.
The U.S. has alleged that al-Qahtani, who military records show is about 28, barely missed becoming the 20th hijacker on Sept. 11, 2001. The Saudi was denied entry into the country by immigration agents at the airport in Orlando, Florida.
At the time, he had more than US$2,400 in cash, no return plane ticket and lead hijacker Mohamed Atta was waiting for him, the military has said.
Separately Monday, Gordon said the Pentagon has not decided whether to appeal a ruling that ousted a top legal official from a detainee case scheduled to become the first to go to trial at Guantanamo Bay.
In a ruling last week, a military judge at Guantanamo found that Air Force Brig. Gen. Thomas Hartmann, the legal adviser for the tribunals, lacks neutrality and should not participate in the case against a Yemeni who is a former driver for Osama bin Laden. His trial is set for June 2.