Colonel Jorge Mendonca, 41, is among seven soldiers facing military trial in relation to events that led to the death of Baha Mousa, a 26-year-old hotel receptionist who died in the custody of the Queen's Lancashire Regiment in Basra in September 2003.
Yesterday, Louise Mendonca claimed her husband had been let down by the Army because there was a "real or perceived pressure" to put officers in the dock after the courts martial of junior ranks in a separate prosecution this year.
She claims the case against her husband, who is accused of neglect in failing to ensure the safety of Iraqi prisoners held under his command, appeared to progress no further until after the "Camp Breadbasket" trial. A court martial in Osnabrück, Germany, which centred on detainee abuses at the food camp near Basra, was labelled a "farce" by representatives of the alleged victims.
After the case General Sir Michael Jackson, the head of the Army, appointed Brigadier Robert Aitken to "track any subsequent prosecutions and report to me with recommendations for action".
On 2 March, Brigadier Aitken wrote to commanding officers who had served in Iraq: "The media ... is giving our military discipline system a bit of hammering and is also asking ... whether our officers behaved to the highest standards. Do you have any evidence of officer behaviour in Iraq which I could use."
But yesterday, the Ministry of Defence (MoD) defended the military court martial system. A spokes-man for the MoD said the Baha Mousa case would go ahead as planned and would be heard not before September next year.
He said: "It's for the Army Prosecuting Authority to take it forward. But it's not appropriate to comment on The Daily Telegraph story because the case is very much alive." He added the MoD had "full confidence" in the court martial system. "Cases go through the civil courts and they collapse," he pointed out.
According to yesterday's newspaper report, Colonel Mendonca, who denies the allegation, ordered his officers to "over-react at the first instance of soldiers' overstepping the mark". In conclusion, he said the regiment was a "force for good" in Basra and that his soldiers "were rightly very proud of what we achieved".
Three weeks later he was interviewed under caution by the Royal Military Police and two months after that he was formally charged.
Mrs Mendonca said in her interview: "The outcome of his case is largely irrelevant in terms of the irreparable damage being done to the Army. The moment Colonel Jorge Mendoca, DSO, MBE, steps into the dock, he will leave behind a truly broken organisation."