The military justice 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.

The breach prompted Col. Karen Mayberry, the chief military defense counsel, to order all attorneys for Guantanamo detainees to stop using Defense Department computer networks to transmit privileged or confidential information until the security of such communications is assured.

Army Col. James Pohl, the chief judge at Guantanamo, also ordered a two-month delay in pre­trial proceedings in the military-commission case against Abd al-Rahim al-Nashiri, who is accused of organizing the 2000 bombing of the USS Cole in Yemen. Defense attorneys in the trial of Khalid Sheik Mohammed , the professed mastermind of the Sept. 11, 2001, attacks, and four co-defendants filed an emergency motion — via a handwritten note — seeking a similar pause in proceedings.

Pretrial hearings in both cases were set to resume this month.

“Is there any security for defense attorney information?” said James Connell, attorney for Ali Abdul Aziz Ali, one of the Sept. 11 defendants. “This new disclosure is simply the latest in a series of revelations of courtroom monitoring, hidden surveillance devices and legal-bin searches.”

The inappropriate transfer of the e-mails follows other questions about government intrusion and secrecy that have undermined the legitimacy of a judicial process that has struggled to establish itself as an effective forum for the prosecution of some terrorism cases.

In February, a military lawyer acknowledged that microphones were hidden inside devices that looked like smoke detectors in rooms used for meetings between defense counsel and their clients. The military said the listening system was not used to eavesdrop on confidential meetings and had been installed before defense lawyers started to use the rooms. The government subsequently said it tore out the wiring.

That same month, Pohl learned that the soundproofed courtroom at Guantanamo was wired with a “kill switch” that allowed an unknown government entity, thought to be the CIA, to cut audio feed of the trial to the public gallery. Pohl ruled that in the future only he could turn off the audio feed to protect classified information. But defense lawyers questioned whether the audio equipment in the courtroom had been manipulated to allow the government to monitor attorney-
client conversations.

In the latest controversy, the prosecution gained access to about 540,000 e-mails from defense teams. It is not clear which cases or lawyers the e-mails concerned; a Pentagon spokesman declined to comment, citing ongoing litigation.

Defense attorneys said prosecutors told them that they stopped looking at the e-mails as soon as they realized that the messages contained confidential defense information.

The mishandling of the e-mails was detected when IT specialists were conducting a search of the government’s computer system on behalf of prosecutors in a particular case. When they did so, they came across not only the e-mails they were seeking but also those between defense lawyers.

Defense attorneys said military IT personnel unsuccessfully tried to refine their search parameters two more times — and in each case discovered more confidential defense material.

In another controversy, defense counsel recently complained that huge volumes of work files were lost when the Defense Department tried to upgrade its network and mirror at Guantanamo the computer system that is available to defense lawyers handling detainee cases in the Washington area.

“Entire files, months of work was just gone,” said Navy Cmdr. Stephen C. Reyes, an attorney for Nashiri. “I have no evidence of any nefarious conduct, but it demonstrates again that we don’t have confidence that our files and communications are secure.”

Reyes noted that a prosecution file also was recently found in the defense computer system.

The latest delay in the commission hearings comes as the Obama administration faces a widening hunger strike among the detainees at Guantanamo.

Attorneys for the detainees and the military have clashed over the number of participants in the protest. The Pentagon said Thursday that 43 of the 166 detainees were on hunger strike, of whom 11 are being force-fed, while defense attorneys said the overwhelming majority of the 120 or so detainees in Camps 5 and 6 are on hunger strike.

The military has refused requests from the media, including The Washington Post, to allow reporters to observe conditions at the camps. Human Rights groups also have requested unfettered access to the camps.

A team from the International Committee of the Red Cross is visiting the camp, but the organization does not make its recommendations public.

ICRC President Peter Maurer said Thursday in an interview at The Post that the hunger strike is born of detainees’ frustration at being held indefinitely without any further review, even in cases in which they have been cleared for transfer out of Guantanamo.