Seventeen sailors were killed and 47 others wounded when the ship was bombed in Yemen. The vessel was seriously damaged, as well.
The government is seeking the death penalty against Abdel al Rahim al-Nashiri, who was charged with the deaths after being held at the detention center at Guantanamo Bay naval base in Cuba since 2006.
"Conducting fair, just, and open military commissions is the Department of Defense's top legal services priority," the Department of Justice said in a statement.
The legal adviser to the U.S. military commission system, Brig. Gen. Thomas Hartmann, said the case may go forward against al-Nashiri despite questions the evidence against him was obtained through waterboarding, Voice of America reported.
"You have to look at the evidence," Hartmann said. "We will look at the evidence, all the evidence that is associated with the case. While there has been an admission that there was waterboarding, there may well be other evidence in the case."