The battered credibility of the Guantánamo trials has been further dented by revelations of hidden microphones, intelligence service interference with court proceedings and protests from lawyers who say the US military is preventing a proper defence of the alleged organisers of the 9/11 attacks.

The increasingly chaotic pre-trial hearings for the alleged mastermind of the attacks on the World Trade Center, Khalid Sheikh Mohammed, and four co-accused have slowed progress toward the full trial, to the point where it will now not start until at least 2014. But the latest developments also further undermine confidence in a military court whose legitimacy has long been questioned.

In recent days, the commander of the Guantánamo prison, Colonel John Bogdan, was forced to admit on the witness stand that secret listening devices disguised as smoke detectors were installed in the cell where lawyers met their clients, and that he knew nothing about them.

The eavesdropping was revealed in court by one of the defence lawyers, Cheryl Bormann, who said she became suspicious about the supposed smoke detectors during a meeting with her client, Walid bin Atash, who is accused of training some of the 9/11 hijackers.

"I said, Mr Guard, is that a listening device, and he said, 'Of course not'," she said. "Well, guess what, judge? It's a listening device".

The prison's lawyer, Captain Thomas Welsh, told the court he discovered the room was fitted with hidden microphones early last year and reported it to the then warden, Colonel Donnie Thomas, to seek assurances that meetings between the accused and their lawyers were not being spied on.

Bogdan said he was not informed when he took over. He told the court that the FBI was in control of the room until 2008 and that he has since discovered that the bugs were accidentally disconnected in October during renovations but then secretly reconnected by an unnamed intelligence service two months later, suggesting they were still in use.

Bogdan denied that the microphones were eavesdropping on lawyers. "We understood that any listening to an attorney-client meeting is prohibited," he said.

But Daphne Eviatar, senior counsel at Human Rights First who was an observer at the recent pre-trial hearings, questioned whether Bogdan could give that assurance when he claimed not to know about the bugs until recently.

"The commander of the base himself didn't even know that the cells where the attorneys are allowed to interview their clients are all bugged. They all have audio surveillance equipment. That equipment is controlled by the intelligence agencies not the commander of the base. It's not clear who knows what about how it was being used," she said.

Defence lawyers also discovered that the courtroom microphones have an unusual level of sensitivity, raising the prospect that privileged conversations with their clients were also covertly listened to during proceedings.

That followed a strange incident at a hearing last month when the audio feed from the courtroom to the public and reporters was suddenly cut when a defence lawyer made a reference to torture in an unclassified motion arguing that CIA "black sites" in Poland, Afghanistan and Romania, used to interrogate and torture abducted suspects, be preserved.

The judge, Colonel James Pohl, was caught unawares and demanded to know who had cut the feed. It transpired that an unnamed intelligence agency was monitoring proceedings from an unspecified location and decided to censor the hearing, a privilege Pohl said was reserved exclusively for him.

The Pentagon refused to publicly identify who had cut the feed, and whether they were even in the Guantánamo complex.

"What happened in the courtroom was shocking," said one of Khalid Sheikh Mohammed's lawyers, Captain Jason Wright. "There was a wizard behind the curtain who had the power to completely cut off the audio feed to the proceedings, to censor what was being said in court. It would be foolish for us to not consider that capability in other areas where we interact with the accused."

When defence lawyers examined microphones in the courtroom they found them to be unusually sensitive – so much so that they could pick up the conversations of guards chatting at the far reaches of the court.

Bormann described the situation as extraordinary.

"I've been practising law for 25 years and never have I been put in the position where I have to ask the following: 'Am I being listened in as I talk to my client?' My concern is I can't have a communication with my client in this court without it going on the record," she told the court.

Defence lawyers also accused the prison authorities of using cell searches to seize confidential legal documents. Attorneys for three of the accused – Mohammed, Bin Atash and Ramzi Binalshibh – said that the men returned to their cells on Tuesday to discover that the bins they use to store documents had been searched and confidential papers removed.

"We need to stop this now," Bormann said. "This affects our ability to do our jobs."

James Harrington, who represents Binalshibh, said: "It causes an enormous emotional problem which makes our job close to impossible."

The prison lawyer, Lieutenant Commander George Massucco, confirmed that the documents had been removed and said they would be returned shortly. Massucco said the situation was created by a change in the guards, with the navy taking over from the army, resulting in a fresh inspection which led the new guards to remove documents they found "disturbing".

The guards also seized books including a copy of the 9/11 Commission report and a memoir by a former FBI agent, Black Banners, which is critical of torture such as waterboarding, which was used on some of the alleged terrorists.

Bin Atash made an unusual outburst in court over the confiscation from his cell of a picture of the Grand Mosque at Mecca.

"In the name of God there is an important thing for you …" he shouted. The judge cut him off and threatened to remove Bin Atash from the court.

A former military lawyer at the camp testified that he believes he was removed from his post at Guantánamo after raising ethical questions about reading protected communications between the defendants and their lawyers.

The past week's revelations have fed into attempts by defence lawyers to claim they are being prevented from giving a proper defence of their clients and to paint the entire legal proceedings as illegitimate.

Eviatar said some defence lawyers have begun to question whether the constraints on fulfilling their duties – from what they regard as the illegal snooping to constraints on meetings with their clients, curbs on the evidence they can use and the treatment of the accused – means they cannot fulfil their duties.

"What they're saying is they're not able to meet those basic legal and ethical obligations, and that undermines the legitimacy of the entire trial. They're not able to form a relationship with their clients because the client no longer trusts them because they're eavesdropping on them and reading their communications," she said.

"It's a legitimate concern. It really disrupts the ability for the attorney to be able to develop any kind of relationship with the client. If they don't trust their own lawyer it's very difficult for them to participate in their own defence. That's important, especially in a death penalty case."

The former vice admiral in charge of the 9/11 trials, Bruce MacDonald, was forced onto the stand over the dispute.

He got into a spat with one of the defence lawyers who was his junior in rank, Commander Walter Ruiz. Ruiz challenged MacDonald's independence and commitment to a just trial, and suggested he had rushed to pursue the death penalty.

MacDonald said that he and other lawyers in the US navy had been "disgusted" by the military tribunals set up by the Bush administration and they pressed hard to make the system more just, including a bar on evidence obtained through torture.

Defence lawyers say that the use of waterboarding and other abuses should require that the state does not pursue the death penalty.

Eviatar said the military tribunal's track record is already damaged by the use of torture and CIA black sites in interrogations, and the original Bush plans for the conduct of the trials which were struck down by the supreme court as unconstitutional.

"I think what's happening really seriously undermines the credibility of the process," she said. "These are new courts to begin with. The first version of these courts was struck down by the US supreme court so you're already starting with a lot of scepticism. And this current version hasn't been tested in the US supreme court yet. But there's so many problems every step of the way that it's going to be very hard for anyone to look back and say this was a fair trial."