A military judge overseeing September 11 pre-trial hearings has revealed the government has censored them from outside the courtroom, and angrily ordered this stop immediately.

The proceedings at the high-security, high-tech courtroom due to host the trial of five alleged plotters in America's worst terrorist attack are heard in the press gallery and in a room where human rights groups and victims' families sit, with a 40-second delay.

This is done so a court security officer, or CSO, sitting next to the judge can block anything deemed classified.

The officer has two switches - "stop" and "go" - and spectators behind a thick glass window can see a red light go on when proceedings are in fact being silenced.

Judge James Pohl disclosed on Thursday that the government - by means of the so-called original classification authority (OCA) - also has a switch, but outside the courtroom, that allows it to cut off the broadcast of the proceedings.

On Monday part of the proceedings were censored when the discussion touched on secret CIA prisons where the suspects were held and abused.

The judge said he was surprised and angry that the censoring mechanism was activated from outside the court, without his knowledge.

This must stop, Pohl said, adding that "the judge and only the judge" can decide what happens in his courtroom.

Thursday was the last day of the latest session of pre-trial hearings. The five defendants, including self-proclaimed 9/11 mastermind Khalid Sheikh Mohamed, were not present as they are boycotting the sessions.

The 9/11 trial at this US base on the southeastern tip of Cuba is not expected to start for at least a year.

The five men accused of plotting the suicide airliner attacks against the Twin Towers and the Pentagon face the death penalty if convicted. The attacks left nearly 3000 people dead.

Before Pohl's ruling, defence lawyers filed an emergency request seeking to suspend the proceedings on grounds that a dispute over the confidentiality of their conversations with their clients had not been resolved.

David Nevin, lawyer for Mohamed, said all his conversations with his client - including during prison visits and even in the courtroom - are being recorded.

The next hearings are scheduled to begin on February 11, and the confidentiality issue is to be addressed. Pohl has ordered the defendants be present for that hearing.