A colonel acquitted in a trial over the abuse of Iraqi prisoners is understood to have quit the Army because he was to face internal disciplinary action over the same incident.

The wife of Colonel Jorge Mendonca, the most senior soldier in recent history to face a court martial, claimed last night that military chiefs were determined to make him a “scapegoat for the failings of others”.

Colonel Mendonca, 43, was one of seven soldiers charged with abusing nine Iraqi civilians in Basra in 2003. One of the prisoners, Baha Mousa, a hotel receptionist, died.

At the court martial which began in October 2006, prosecutors claimed that Colonel Mendonca had failed to ensure that prisoners in the custody of his unit of the Queen’s Lancashire Regiment were treated properly.

The court martial ended in February with the conviction of Corporal Donald Payne, who was jailed for a year.

Colonel Mendonca’s wife, Louise, 39, said last night that after her husband’s acquittal the Queen had sent him a message of support. She said that despite assurances given to her husband after the court martial that he would not face “administrative punishment”, the military top brass had changed its mind.

“If my husband’s acquittal had been the end of the matter, as it should have been, then he would have continued with his career. But it is now clear to us that there are those within the Army who are still determined to make him a scapegoat for the failings of others,” she said.

“My husband has decided he will not be hounded any more and would rather leave than face further injustice. His integrity, loyalty and family are more important to him than military ambition. He has fallen out of love with the Army – or at least those in charge of it.”

Last month The Times revealed that Colonel Mendonca and another five soldiers would face further inquiries, with the possibility of administrative action – a disciplinary hearing behind closed doors that can lead to an officer’s dismissal.

Colonel Mendonca, who was awarded the Distinguished Service Order in recognition of his “dynamism, leadership and bravery” in Iraq, said in February after his acquittal that he planned to stay in the Army. He said that he had served his country for 25 years as best he could, but that the past two years had been difficult, particularly for his family. He said that he had been privileged to command the Queen’s Lancashire Regiment in Iraq, which worked in “indescribably difficult conditions to make Basra a better place”.

Mrs Menonca told the Daily Mail that his commanders, who were heavily criticised for bringing the original prosecutions, were determined to have a “scalp” for the death of Mr Mousa. She said: “The five-month courtroom farce and the preceding two-year investigation can be described at best as incompetent and at its very worst a complete and utter betrayal. The last two years have been monstrously unfair on a dedicated and patriotic soldier. They have also been tremendously painful and difficult for myself and our two young sons.”

She said the couple had been overwhelmed with messages of support after his acquittal. “Perhaps the most moving was a personal message directly from the Queen to say how delighted she was at Jorge’s acquittal.”

At the court martial, which is estimated to have cost up to £20 million, only one of the seven original defendants, Corporal Payne, was convicted of an offence arising from the alleged detention and beating of the Iraqis that led to Mr Mousa’s death. He pleaded guilty to the war crime of inhumane treatment of detainees under the International Criminal Court Act 2001.

The Ministry of Defence said last night that it never discussed the careers of individual soldiers but acknowledged that General Sir Richard Dannatt, the head of the Army, had said after the court martial that the prosecuting authority and the Royal Military Police would consider whether further investigation was appropriate.

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