Officials said on Sunday there was no evidence Lieutenant General Ricardo Sanchez or other senior military officers were aware of the prisoner abuse while it was happening.
"There was a news report published May 23 2004, which suggests that Lt Gen Ricardo Sanchez, commander of Multinational Forces-Iraq, was aware of, and in some instances, present at Abu Ghraib while detainee abuse was occurring," the US military said.
"This report is false." Prison officials blamed the abuse on low-level military police, some of whom maintain they were just following orders.
Beg to differ
But a military police commander at Abu Ghraib prison is to testify the top US general in Iraq witnessed some of the abuses.
The Washington Post on Saturday quoted a military lawyer as saying Captain Donald Reese told him Sanchez and other senior military officers were aware of the abuse at the prison.
The military lawyer, Capt Robert Shuck, is assigned to defend Staff Sgt Ivan "Chip" Frederick of the Army Reserve's 372nd Military Police Company.
Frederick is one of the seven members of the company facing criminal charges for abusing Iraqi inmates. Reese is the company commander.
According to the transcript of an open hearing on 2 April at Camp Victory in Baghdad, Shuck said Reese told him General Sanchez was present and witnessed some of the abuse.
"Are you saying that Captain Reese is going to testify that General Sanchez was there and saw this going on?" Shuck was asked by a military prosecutor according to the transcript.
"That's what he told me," Shuck replied. "I am an officer of the court, sir, and I would not lie. I have got two children at home, I am not going to risk my career," he said.
When contacted by the Washington Post, Brig Gen Mark Kimmitt, the senior military spokesman in Iraq, said Sanchez was unavailable for comment, but would respond later.
The transcript marks the first allegation Sanchez or other senior military officers were aware of the prisoner abuse while it was happening.
In another prison abuse scandal, an Iraqi scientist reputedly close to Saddam Hussein died while being held at a US base in Baghdad, according to a British newspaper report on Monday.
Professor Muhammad al-Izmirly died of "brainstem compression", according to an official diagnosis by US military doctors, The Guardian newspaper said.
But according to Faik Amin Bakir, head of the autopsy service at Baghdad hospital, the scientist died from a sudden blow to the back of the head.
"I will hate Americans and British people for the rest of my life. You are democrats. You said you were coming to bring democracy to Iraq, and yet you killed my father"
daughter of Prof al-Izmirly
"He died from a massive blow to the head. We don't disagree with the coalition's report but it doesn't explain how he got his injuries in the first place," the paper quoted him as saying.
The death certificate with the body, which was delivered to the Baghdad morgue and identified only by the number 1909, did not mention the skull fracture.
Arrested on 26 April 2003 at his home in Baghdad, al-Izmirly
was held for almost nine months by US forces before his family was able to visit him on 11 January 2004.
"When I saw him, his health was good. I asked the Americans why they had arrested him. They told me simply 'he is a witness' ", one of his daughters, Rana told The Guardian.
Barely a month later, on 19 February, the Red Cross announced his death to the family.
"I will hate Americans and British people for the rest of my
life. You are democrats. You said you were coming to bring democracy to Iraq, and yet you killed my father," Rana said.
"You offer no proof that he did something wrong, you refuse him a lawyer, and then you kill him. Why?"