Charges have been dropped against five out of seven soldiers on trial for abusing Iraqi civilians.
Col Jorge Mendonca was cleared of all charges, along with three of his men.
A fifth soldier who had admitted mistreating Iraqi detainees in Basra was cleared of further charges.
The court martial at Bulford Camp in Wiltshire is dealing with claims soldiers abused detainees in September 2003, resulting in an Iraqi's death.
Col Mendonca, 43, former commander of the Queen's Lancashire Regiment and the highest-ranking British serviceman in recent history to face court martial, had faced charges of negligently performing a duty.
Col Mendonca, who won a DSO (distinguished service order) in the Gulf, said he remained convinced his soldiers did "enormous good" in Basra in 2003.
"Every one of my soldiers and officers worked extremely hard under indescribably difficult conditions to make Basra a better place, and I just hope that fact is not forgotten in the aftermath of this trial," he said.
CHARGES IN FULL
Col Jorge Mendonca - cleared of negligently performing a duty
Sgt Kelvin Stacey - cleared of common assault
L/Cpl Wayne Crowcroft - cleared of inhumane treatment
Pte Darren Fallon - cleared of inhumane treatment
Cpl Donald Payne - admitted inhumane treatment, cleared of manslaughter and perverting the course of justice
Warrant Officer Mark Davies - charged with negligently performing a duty
Maj Michael Peebles - charged with negligently performing a duty
The trial has been dealing with claims that some of the colonel's men abused a group of Iraqis arrested at a Basra hotel where the army had found weapons and suspected bomb-making equipment.
The prosecution said that while undergoing so-called conditioning for interrogation, the group were forced to stand in the stress position - with arms outstretched and knees bent - and were beaten if they failed.
Baha Mousa, 26, was among the group of detainees and later died. It was found he had 93 separate injuries to his body.
But Mr Justice Stuart McKinnon ordered Col Mendonca and the others to be cleared because of a lack of evidence.
Shadow defence secretary Liam Fox said the trial had been of "enormous expense to the taxpayer" and questioned whether the charges should have been brought in the first place.
Conservative MP Ben Wallace, trained by Colonel Mendonca when he was an instructor at Sandhurst, said the trial was a "political-driven initiative" to "satisfy public doubts in the Iraq conflict".
But a spokesman for the Attorney General's office said there was "no question" of the prosecution having been influenced by political pressure.
BBC correspondent Paul Wood said: "The use of the stress position was allowed back in 2003.
"The question for the coalition then, and for this court today - what is a legal and proper method of interrogating prisoners."
Sergeant Kelvin Stacey, 30, of the QLR, was cleared of assault occasioning actual bodily harm and common assault.
L/Cpl Wayne Crowcroft, 22, and Private Darren Fallon, 23, both of the QLR, now merged with the Duke of Lancaster's Regiment, were both cleared of treating Iraqis inhumanely.
Hotel receptionist Baha Mousa died in custody in 2003
Cpl Donald Payne, 35, of the QLR, has already pleaded guilty to inhumanely treating civilian Iraqi detainees, and faces sentencing.
But he was cleared of manslaughter and of perverting the course of justice.
Maj Michael Peebles, 35, and Warrant Officer Mark Davies, 37, both of the Intelligence Corps, remain on trial.
They both deny charges of negligently performing their duty.
The trial was adjourned until Monday.