Washington: A deeply frustrated military judge on Friday halted the effort to use a military tribunal to prosecute a Guantanamo Bay detainee accused of orchestrating the 2000 bombing of the US destroyer Cole, bringing the troubled case to an indefinite standstill.

The judge, Colonel Vance Spath of the Air Force, suspended pretrial hearings in the death penalty case against the detainee, a Saudi named Abd Al Rahim Al Nashiri, after nearly the entire defence team quit late last year in a dispute over whether their attorney-client communications were subject to monitoring. The lawyers defied his orders to return, citing ethical obligations.

“I am abating these proceedings indefinitely,” Spath said, according to a transcript. “I will tell you right now, the reason I’m not dismissing — I debated it for hours — I am not rewarding the defence for their clear misbehaviour and misconduct. But I am abating these procedures — these proceedings indefinitely until a superior court orders me to resume.”

A Pentagon spokeswoman, Commodore Sarah Higgins, said it was “unknown when pretrial hearings will begin again.”

The Miami Herald first reported Spath’s decision.

Al Nashiri was arraigned in 2011 in a case that centres on a ship attack that killed 17 sailors. His is one of two capital cases in the military commissions system, alongside the attempt to prosecute five detainees who were arraigned in 2012 on charges of aiding the September 11 attacks. Both cases have been stuck in pretrial hearings.

When the Bush administration created the military commissions system in 2001, a debate erupted that was centred on individual rights. Proponents saw the tribunals as a means for meting out swift justice to terrorists, while human rights advocates feared that they would run roughshod over fair-trial protections.

As the years have passed, however, the focus has shifted to effectiveness. While the commissions system has achieved several convictions through plea deals, it has struggled to get contested cases to trial, and has been costing taxpayers about $100 million (Dh367.3 million) a year for three cases covering seven defendants. (Its third pretrial case is against an Iraqi detainee who was arraigned in 2014; he is not facing capital charges.)

By contrast, civilian court prosecutors have routinely gotten terrorism cases to trial relatively quickly and won harsh sentences. On Friday, for example, a federal judge in Brooklyn sentenced an Al Qaida terrorist known as Spin Ghul to life in prison for killing two US service members in Afghanistan and for plotting to bomb a US Embassy in West Africa; he was convicted in March after a civilian court trial.

According to the transcript in the Cole case, Spath said the events that had led to its derailment “have demonstrated significant flaws within the commissions process,” and he accused defence lawyers of trying to block the system rather than working within it.

Citing his 26 years working in the regular court-martial system, he also described himself as “shaken” by the experience and portrayed Al Nashiri’s one-time defence lawyers as pursuing a “revolution to the system” by defying judicial orders.

Earlier in the week, he had weighed having US marshals seize two of Al Nashiri’s former lawyers — both civilian employees of the Pentagon — to force them to appear by video link from Virginia after they failed to comply with subpoenas, but decided against it.

On Friday, he argued that in his efforts to get Al Nashiri’s defence lawyers back to work on the case, “I’m not ordering the Third Reich to engage in genocide — this isn’t My Lai.” And he said he was weighing imminent retirement.

The latest trouble began in June, when Al Nashiri’s defence team discovered something in a room where they talked with their client. The details remain classified, but after Spath rejected the notion that there was a problem and tried to proceed, the civilians on Al Nashiri’s defence team quit in October, saying they had an ethical conflict.

That left only a junior, uniformed defence lawyer, Lieutenant Alaric Piette of the Navy. Piette has continued to appear in court but has not participated, arguing that he was unqualified and that the presence of a “learned counsel,” or death penalty specialist, is necessary — a contention Spath rejected.

Spath in November declared Brigadier General John Baker, who oversees military commissions defence lawyers, in contempt of court for refusing to order the two civilian Pentagon employees to resume work on the case. The general argued that he had the authority to dismiss them without the judge’s consent — another contention Spath rejected.

Spath ordered Baker confined to a trailer and fined him, but after several days, Harvey Rishikof, a former civilian Pentagon official who was then the convening authority overseeing the commissions system, freed the general and overturned the fine, although he left the contempt finding in place.

In doing so, Rishikof also recommended that the military build or designate a “clean” facility to provide confidence that “the attorney-client meeting spaces are not subject to monitoring.” (This month, Defence Secretary Jim Mattis abruptly fired Rishikof without explanation.)

On Thursday, Spath questioned Paul S. Koffsky, a senior civilian Pentagon lawyer who oversees the office of military commissions defence lawyers. Koffsky told the judge that he only writes performance appraisals and does not tell defence lawyers what to do, and had not read the filings about the confidentiality dispute, a transcript shows.

“We need action from somebody other than me, and we’re not getting it,” Spath said Friday, adding, “We’re going to spin our wheels and go nowhere until somebody who owns the process looks in and does something.”

Richard Kammen, a civilian defence lawyer who had been the death penalty specialist for Al Nashiri before quitting, said: “We’re certainly gratified that ultimately Judge Spath reached the correct decision that the case needs to stop. This should have happened months ago.”

Piette said he expected the case to resume this year, probably without Spath as the judge. In the meantime, he said, he would try to take death penalty courses and get caught up on years of rulings in the case.

“I’m cautiously pessimistic,” he said. “Things happen here that don’t go on in normal courts, and this is one. A judge just called ‘time out’ for no clear legal reason. I don’t know how it will play out, but it will probably somehow be worse.”