Already postponed due to the Muslim holy month of Ramadan and a technical glitch, the hearings were to have begun Thursday and run through August 28, but Judge James Pohl delayed them "due to weather" without setting a new date.
Tropical Storm Isaac, currently battering the Lesser Antilles, could become a hurricane by Thursday and is expected to hit eastern Cuba by early Saturday, according to the Miami-based National Hurricane Center.
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Self-proclaimed 9/11 mastermind Khalid Sheikh Mohammed and several of his alleged deputies have been detained at the US-run Guantanamo prison since 2006 after being held at secret CIA-run prisons where they say they were tortured.
Their trial is not expected to begin for at least a year, after a series of preliminary hearings.
Commanders at Guantanamo have meanwhile ordered hurricane preparations.
Navy Captain Robert Durand, a spokesman at the facility, said the exact measures are classified but "not unlike the preparations familiar to anyone living in a hurricane zone."
Authorities will be distributing handheld radios and generators and making sure there are no loose objects that could become "missile hazards" in high winds, he said.
He added that 85 percent of Guantanamo prisoners live in "brick-and-mortar structures capable of withstanding hurricane-force winds" and that all detainees would be kept in secure locations in the event of a storm.
Some 6,000 people live and work on the military base, in addition to the 168 detainees, who are suspected of belonging to Al-Qaeda.
The United States began using the prison in 2002 to hold alleged Al-Qaeda militants captured in Afghanistan and other newly charted battlefields in the global war on terror.
Mohammed is on trial along with his Pakistani nephew Ali Abd al-Aziz Ali, also known as Ammar al-Baluchi; Mustafa al-Hawsawi of Saudi Arabia; and Yemenis Ramzi Binalshibh and Walid bin Attash.
The five face the death penalty if convicted for their roles in the September 11, 2001 attacks, in which hijackers crashed planes in New York, Washington and Shanksville, Pennsylvania, killing 2,976 people.
