Brig. Gen. Thomas W. Hartmann, legal adviser to the U.S. military tribunal system, said charges are being sworn against Abd al-Rahim al-Nashiri, a Saudi of Yemeni descent, who has been held at the military prison in Guantanamo Bay, Cuba, since 2006.
The charges still must be approved by a Defense Department official who oversees military tribunals set up for terrorism suspects.
Hartmann said the allegations include conspiracy to violate laws of war, murder, treachery, terrorism, destruction of property and intentionally causing serious bodily injury.
Seventeen American sailors were killed when the Norfolk, Va.-based Navy destroyer was attacked in the Yemeni port of Aden as it refueled.
Al-Nashiri told a hearing at Guantanamo Bay last year that he confessed to helping plot the bombing only because he was tortured by U.S. interrogators.
CIA Director Michael Hayden said early this year that al-Nashiri was among terrorist suspects subjected to waterboarding in 2002 and 2003 while being interrogated in secret CIA prisons.
Asked at a Pentagon press conference how a trial could go forward under those circumstances, Hartmann said all evidence - including the issue of torture or abuse - would be before the tribunal.
Last October, Yemen set free one of the al Qaeda masterminds of the attack. Jamal al-Badawi, who is wanted by the FBI, was convicted in 2004 of plotting, preparing and helping carry out the USS Cole bombing and received a death sentence that was commuted to 15 years in prison.
Al-Badawi had escaped prison once before with nine other suspects of the attack on the Norfolk-based Cole in April 2003, but was rearrested.
Al Qaeda used to have an active presence in Yemen, the ancestral home of Osama bin Laden. The group was blamed for the bombing of the Cole and the attack on a French oil tanker that killed one person two years later.