The decision to prosecute three junior soldiers for war crimes against Iraqi prisoners while pressing lesser charges against their seniors was "deeply unfair", a court martial was told yesterday.

Three soldiers had been "singled out" to "shoulder the blame" for the brutal treatment meted out by many other colleagues - and sanctioned by officers, it was claimed.

The three junior soldiers are accused of the inhuman treatment of a group of Iraqi civilians, a war crime which carries a maximum 30-year prison term. But three officers face charges of neglecting their duty by not preventing the ill-treatment, for which they can be jailed for no more than two years.

Tim Owen QC, the barrister for Corporal Donald Payne, who is said to be at the centre of the alleged abuse, said it was "extraordinary" that the junior soldiers had been targeted when they were carrying out the orders of their seniors. He said: "Three individuals have been singled out. It is [the prosecution] case that they and they alone must shoulder the blame for the wholly unacceptable treatment meted out to the detainees.

"There is something deeply unattractive, deeply unfair about a prosecution which applies one set of rules to the junior ranks, those operating at the sharp end, and a very different set of rules to those higher up the chain of command."

The court martial has been told how a group of Iraqi civilians was beaten while hooded and handcuffed after being seized in a raid on a hotel in Basra, southern Iraq, in September 2003. One man, a hotel worker, Baha Musa, was allegedly killed by Cpl Payne. He denies manslaughter but has pleaded guilty to a war crime.

Making an initial defence statement on Cpl Payne's behalf, Mr Owen accepted that the soldier had kicked, punched, prodded and slapped prisoners and forced them to maintain painful "stress positions".

He also conceded that Cpl Payne had organised what was nicknamed "the choir" - prisoners were beaten in turn to elicit a range of grunts and groans. "Horrible though it sounds to say in the clinical atmosphere of this court room, this did become something of a sick joke among the soldiers," said Mr Owen. He said Cpl Payne believed he was "conditioning" the prisoners - preparing them for questioning - "something which was known of and approved by his superiors".

Giving an opening statement on behalf of the men's commanding officer, Colonel Jorge Mendonca, Timothy Langdale QC strongly rejected that he had negligently performed his duty by not stopping the ill-treatment.

Mr Langdale also gave an insight into the "highly exceptional" and "hugely challenging" conditions Col Mendonca's battalion, the 1st Battalion The Queen's Lancashire Regiment, was operating in.

Mr Langdale said Col Mendonca's commanding officer, Brigadier William Moore CBE, late of the Royal Artillery, would tell the court martial there was a "distinct lack of support" from Whitehall.

Mr Langdale said it was "inevitable" that Col Mendonca would have to prioritise and delegate - but he had not turned a blind eye to abuse.

Five other soldiers, along with Cpl Payne and Col Mendonca, face charges. A lance corporal and a kingsman deny inhumanly treating the Iraqis and a sergeant denies assault. Two other officers, a major and warrant officer, deny negligently performing a duty. The court martial at Bulford Camp, Wiltshire, continues today when the first witnesses will be called