Among them is Khalid Sheikh Mohammed, who has portrayed himself as the mastermind of the attacks.
Prosecutors want the U.S. military judge to consider security rules in advance of the trial to prevent the accused from publicly revealing what happened to them in the CIA's secret network of prisons. Defense lawyers say the security rules will hamper their case.
The American Civil Liberties Union, which has filed a challenge to the protective order, says the restrictions will prevent the public from learning what happened to Mohammed and his co-defendants during several years of CIA confinement and interrogation.
Protective orders are standard in civilian and military trials to set rules for handling evidence for the prosecution and defense.
Army Brig. Gen. Mark Martins, the chief prosecutor for the military commissions, said Sunday that security precautions are necessary to keep information from getting out that could endanger U.S. intelligence operations or personnel around the world. He also said the precautions are not aimed at preventing a government embarrassment or to cover-up wrongdoing.
"Our government's sources and methods are not an open book," Martins said.
The judge's approval of the protective order, which may not happen this week, must occur before the Sept. 11 case can move forward.
The preliminary trial is expected to run through Friday. The families of people killed in the Sept. 11 attacks have been invited to military installations around the country to watch the pretrial hearings, which are closed to the general public.
Mohammed's four co-defendants include Ramzi Binalshibh, a Yemeni, who was allegedly chosen to be a hijacker but couldn't get a U.S. visa and ended up providing assistance such as finding flight schools; Waleed bin Attash, also from Yemen, who allegedly ran an al Qaeda training camp in Afghanistan and researched flight simulators and timetables; Mustafa Ahmad al-Hawsawi, a Saudi accused of helping the hijackers with money, Western clothing, traveler's checks and credit cards; and Abd al-Aziz Ali, a Pakistani national and nephew of Mohammed, who allegedly provided money to the hijackers.
The Associated Press contributed to this report.