The Defense Department said charges have been filed to a military commission in the case against Mohammed, Walid Muhammad Salih Mubarak bin Attash, Ramzi Binalshibh, Ali Abdul Aziz Ali and Mustafa Ahmed Adam al-Hawsawi.
The five could face the death penalty if found guilty in the 2001 terror attacks in New York, Washington, D.C., and Shanksville, Pa., that resulted in the deaths of 2,976 people.
Mohammed, a Kuwaiti-born, al-Qaida militant captured in Pakistan in 2003, has claimed to be the mastermind behind the attacks. He and his alleged co-conspirators are charged with terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, intentionally causing serious bodily injury and destruction of property in violation of the law of war.
The chief judge of the Military Commissions Trial Judiciary will assign a military judge to the case and the five accused will be arraigned at Naval Station Guantanamo Bay, Cuba, within 30 days, the Defense Department said Wednesday in a release.
The five men have been provided with defense counsel "possessing specialized knowledge and experience in death penalty cases," the Defense Department said.
U.S. Attorney General Eric Holder had wanted to prosecute them in a federal court in New York, but was thwarted by restrictions mandated by Congress on the transfer of prisoners from Guantanamo to the United States.
The accused conspirators initially had been charged before a military commission at Guantanamo but their trial was halted in January 2009 when President Obama froze all tribunal proceedings at Guantanamo pending a review of counter-terrorism policies.
The president last year announced his decision to resume military tribunals at Guantanamo Bay.
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