(Adds tribunal background, ACLU comment, paragraphs 9-12)
WASHINGTON, May 13 (Reuters) - The Pentagon said on Tuesday it dropped charges against a Saudi who U.S. officials say intended to be the "20th hijacker" on Sept. 11 but sent five others to trial on accusations they planned the 2001 attacks.
A Pentagon appointee who oversees the U.S. war court at its Guantanamo Bay military prison did not say why she rejected the charges that prosecutors sought earlier this year against Mohammed al-Qahtani.
She dismissed the charges "without prejudice," a distinction that allows the U.S. government to try to bring charges against Qahtani again.
Murder and conspiracy charges against the five other men accused of planning the attacks, including Khalid Sheikh Mohammed, were approved, the Pentagon said. That means the men, all held at Guantanamo, must be arraigned within 30 days.
They will be tried together in proceedings that should start within 120 days. If convicted, they may face the death penalty.
"What we are announcing today is the next step, which is the referral of charges," said Pentagon spokesman Bryan Whitman.
U.S. military prosecutors first recommended charges in February against the detainees -- Mohammed, Qahtani, Ali Abdul Aziz Ali, Ramzi Binalshibh, Mustafa Ahmed al-Hawsawi and Walid bin Attash.
The charges include conspiring with al Qaeda to murder civilians and 2,973 counts of murder, among others.
The Guantanamo tribunals are the first U.S. war crimes tribunals since World War Two. They were established after Sept. 11 to try non-American captives whom the Bush administration considers "enemy combatants" not entitled to the legal protections granted to soldiers and civilians.
The American Civil Liberties Union has criticized the military commissions system as inherently unfair to defendants, in part because it allows the use of hearsay and secret evidence to yield convictions.
The group on Tuesday said the U.S. government had still not provided necessary security clearances to two civilian attorneys who want to represent Mohammed, better known as KSM.
"The government's failure to provide the necessary clearances to lawyers who have already been cleared for other national security cases is yet another example of the government's obstructing this process and stacking the deck in its favor," said Anthony Romero, ACLU executive director.
Mohammed has said he planned every aspect of the Sept. 11 attacks. But his confession could be a problem if used as evidence because the CIA has admitted it subjected him to "waterboarding" -- an interrogation technique that simulates drowning and has been widely criticized as torture.
U.S. officials say Qahtani tried to enter the United States on Aug. 4, 2001, but was stopped by immigration officials at a Florida airport and placed on a flight out of the country. He was later captured in Afghanistan. (Editing by Eric Walsh)
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