Husain Rashid Mohammed al-Tikriti said he was beaten up after being thrown out of court last Thursday. He punched one of the guards who escorted him after he complained about the expulsion of Saddam.
"I was beaten in the presence of the Americans," al-Tikriti said.
Raed Juhi, the court spokesman, denied the allegation. "The Iraqi police in charge of this are well trained in respecting human rights, and no police officer has beaten up any of the defendants," Juhi said.
Al-Tikriti also complained that the trial was rigged, saying: "The court, prosecution and the Americans are our opponents ... we are confident that the verdict was issued in advance."
International human rights groups have raised concerns about the possibility of a fair trial for Saddam, particularly since the Shia-led government dismissed the chief judge last month after he stated that the former president was not a dictator.
Al-Tikriti is one of five former military commanders on trial with Saddam and his cousin, Ali Hassan al-Majeed, for their alleged role in the Anfal (Spoils of War) campaign that prosecutors say left 182,000 ethnic Kurds dead or missing.
The trial continued with testimony from two Kurdish witnesses on Thursday.
One witness told the court that guards had cut off the water supplies to Kurdish detainees in a desert prison in the south of Iraq.
"We went to beg Hajjaj [a prison guard who has been referred to in the accounts of several witnesses] to give us water and he just said 'we cut the water so you die, you come here to die'," Abdullah Said said.
Said added that 1,800 people died during his time in detention. "I myself helped bury 20 dead prisoners," he said.
He described how it seemed as though all of Kurdistan had been brought to the prison, and in one case a woman gave birth on the ground after a truck left a group in the prison yard.
"Since the days of Adam and Eve, no nation suffered like our nation"
A second witness said that the dirty water they were finally given made them sick and gave them diarrhoea.
"When the doctor came to check us, he said we had cholera," Baqr Qadr said. "Since the days of Adam and Eve, no nation suffered like our nation."
On Wednesday, witnesses described for the first time how detainees were taken to a remote desert location at night and executed.
Two anonymous witnesses told how they were crammed into filthy trucks for hours without water and driven along a dirt road into the desert before the trucks stopped.
"Then we heard the sound of gunfire and we knew it was the people in the next vehicle being shot and that our turn would be next," one witness said.
Somehow the witnesses escaped, after struggling with their guards, and told their stories to human rights organisations.
The judge has adjourned the trial until October 30, after the Eid holiday which marks the end of Ramadan.