Brigadier-General Rick Baccus has also lost his job at the Rhode Island National Guard, amid reports he was too hard on troops while being soft on the prisoners suspected of fighting for the Taleban in Afghanistan.
He left the detention centre at Guantanamo Bay in Cuba on 9 October, it has emerged, five days after a report in the Washington Times newspaper quoted Pentagon sources as saying he was "too nice" to prisoners.
The US Army said General Baccus had been replaced as part of a reorganisation of Camp Delta - where prisoners were moved from Camp X-Ray earlier this year - but his Rhode Island commander added that he had lost confidence in him.
Interrogations 'undermined'
Sources quoted in a number of US newspapers said General Baccus, 50, often clashed with other senior officers at the camp, including Major-General Michael Dunlavey who is in charge of interrogating the prisoners.
The Washington Times said General Baccus irritated General Dunlavey with his decision to allow the Red Cross to put up posters advising detainees they need only provide their name, rank and number during questioning.
The newspaper's sources said General Baccus was undermining the interrogation efforts by his treatment of the detainees, to whom he would say "peace be with you" before each loudspeaker address.
In August, General Baccus told visiting journalists that uniformed officers were concerned that the inmates continued to be considered as "enemy combatants" rather than "prisoners of war", a designation which would give them extra rights.
General Baccus told news organisations in his home state of Rhode Island that he had not interfered with interrogations overseen by General Dunlavey.
The running of the whole camp - detention and interrogation - is now being handled by General Dunlavey pending the arrival of another general set for next month in a reorganisation by the US Army's Southern Command.
Troop complaints
A total of 598 detainees are being held at the camp - where new cells are being built - all suspected of being fighters for the ousted Afghan Taleban regime or members of al-Qaeda which is blamed for the 11 September attacks on the US last year.
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I relieved him... for various reasons, but they all culminated in my losing trust and confidence in him as a commander
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Major-General Reginald Centracchio
The Washington Post newspaper reported that some soldiers at Guantanamo Bay had complained that General Baccus was unresponsive to their concerns about long hours and uncomfortable tent living conditions.
His superior at the Rhode Island National Guard, Major-General Reginald Centracchio, was angry that General Baccus had not kept his headquarters apprised of how troops were doing.
In one case, a Rhode Island guardsman was flown out of Cuba for an emergency appendectomy, but General Centracchio was not informed until the soldier's family contacted him.
General Centracchio said he has stripped General Baccus of his duties as head of military police.
"I relieved him... for various reasons, but they all culminated in my losing trust and confidence in him as a commander".