The military commission system at Guantanamo Bay, Cuba, which has been dogged by charges of secret monitoring of proceedings and defense communications, became embroiled in a fresh controversy Thursday when it was revealed that hundreds of thousands of defense e-mails were turned over to the prosecution.

Col. Karen Mayberry, the chief military defense counsel, ordered all defense lawyers with cases at Guantanamo to stop using Defense Department information systems to transmit privileged or confidential information until the security of such communications is assured.

After learning about the security breach, Army Col. James Pohl, the chief judge at Guantanamo, ordered a two-month delay in pre-trial proceedings in the case against Abd Al Rahim Al Nashiri, who is accused of organizing the 2000 bombing of the USS Cole in Yemen. Defense lawyers in the trial of Khalid Sheik Mohammed, the self-professed mastermind of the Sep. 11, 2001, attacks, and four co-defendants filed an emergency motion — via a handwritten note — seeking a similar pause in proceedings.