Hearings resume but military prosecutors want judges to freeze three cases for review.
Time to speak
Bob Swann, a US military prosecutor, said the US government believed the detainees should attend all sessions.
He requested that Henley grant Mohammed and the other two detainees five minutes of speaking time to encourage them to attend.
The hearing is set to go ahead later on Thursday.
The issue of whether a defendant must attend all sessions at the Guantanamo war court in Cuba has not been resolved.
Military judges have in the past instructed guards to forcibly bring detainees to court, while on other occasions the accused have been permitted to miss the sessions.
All five men accused of a role in the September 11 attacks are charged with murder and other crimes.
They face a possible death sentence if convicted.