In little more than a month from now the British system of military justice will take centre stage as never before.

More than a year after they were charged in connection with the death of an Iraqi hotel worker, Col Jorge Mendonca and six other servicemen will finally appear before a court martial.

But the judge chosen to preside at their trial has never sat in a military court before. In March, it emerged that the case would be heard before a highly-experienced civilian judge, Mr Justice McKinnon.

John Reid, who was Defence Secretary at the time, let it be known that he was furious that Judge Blackett, the senior military judge, had decided not to hear the case - creating what Mr Reid regarded as the false perception that the military system of justice could not cope.

Why then did Judge Blackett, 51, a circuit judge, ask the Lord Chief Justice to assign a more senior member of the judiciary to the case?

"This is the first case brought under the International Criminal Court Act 2001," Judge Blackett tells me. Col Mendonca is not charged under this legislation: the former CO of the Queen's Lancashire Regiment is accused under the Army Act of negligently performing his duty by failing to take any steps, or any reasonable steps, to ensure that civilians were not ill-treated at a holding centre under his command.

But three other members of the regiment are accused of inhumanely treating named Iraqi civilians, a war crime under the Act of 2001. "I believe that this is such an important issue of jurisprudence that a High Court judge should deal with it," Judge Blackett says. All courts martial are now headed by civilian judges. And it is normal practice in the civilian courts for High Court judges to conduct particularly demanding trials.

Judge Blackett is clearly keen to bring courts martial up to the same standard as their civilian counterparts. For this reason, he has ended the age-old practice of judges sitting alongside the military officers who decide, alone, whether the defendant is guilty. This so-called "panel" is, broadly speaking, the equivalent of a jury and so Judge Blackett has directed that all panels should now sit separately from the judge advocate in what amounts to a jury box. The panel members must be senior in rank to each of the defendants. For that reason, the panel in Col Mendoca's case will be headed by a major-general, with the other members being brigadiers and officers promoted to colonel before him.

The trial will take place at a new military court centre in Bulford, near Salisbury - designed to be as open to the public as any civilian court.

Having a military jury is now the main difference between a court martial and a civilian trial.

The panel can put the charges into a military context, Judge Blackett explains. They are just as vulnerable to prejudicial publicity as a civilian jury, he insists, and so the normal rules of contempt of court apply.

The most senior member of the panel, known as the president, is responsible for ensuring that the trial is conducted in a manner that befits the traditions of the Service. But the most dramatic difference between a military panel and a civilian jury is that, after a conviction, the panel will join the judge on the Bench and decide the sentence.

This sounds rather alarming. All the judge advocates are civilians and Judge Blackett has made sure that they are trained to the same level as other judges. But the officers who make up the panel have no such training. For this reason, Judge Blackett has written a detailed guide to sentencing in courts martial.

This tells panel members that they can outvote the judge: only a simple majority is needed. In practice, Judge Blackett says, he will suggest the range within which he believes the sentence should fall, before opening it up to the panel for discussion. If it was up to him, sentencing would be a matter for the judge alone. "But the military are very keen that there should be a military aspect to sentencing and they are not ready to move to sentencing by judge advocates," he says.

That is partly a matter of experience. Four of eight full-time judge advocates - and most of the 12 part-time military judges - have never served in the Armed Forces. The Judge Advocate General, however, was in the Royal Navy for 31 years.

Joining as a cadet, Jeff Blackett read law at university before becoming a supply officer in the Navy. He was then selected by the Navy to read for the Bar, becoming one of a team who advised the commanding officers when they used to preside over courts martial.

By 1991 Judge Blackett was sitting part-time as a uniformed judge advocate. To gain more experience, he served as a part-time stipendiary magistrate in London. He was promoted on both fronts, becoming Chief Naval Judge Advocate while sitting as a Recorder in the Crown Court.

In 2003 the European Court of Human Rights ruled that Naval officers did not qualify as independent and impartial tribunals, putting an end to the post of Naval Judge Advocate. Cdre Blackett left the Navy in 2004 on his appointment as Judge Advocate General.

His unique background has given him an insight into what may prove to be a problem in some future military conflict. There is said to be no risk that British troops will ever be brought before the International Criminal Court in The Hague because charges may be brought only if Britain is unwilling or unable to bring a prosecution itself. The 2001 Act gives our prosecutors full power to do so.

But what if troops have been advised that it would be lawful to bomb a particular target, and that advice is regarded by the ICC as wrong? Britain would not be able to prosecute its own troops for obeying orders, leaving them vulnerable to proceedings in The Hague.

"It's a theoretical and academic point," Judge Blackett insists. The political realities are such that it is not going to happen in the foreseeable future.

True. But Service people should always expect the unexpected.