Chief prosecutor Jaafar al-Mousawi said "no one in the court attacked Saddam or punished him and we will never allow anyone in the court to harm any of the defendants, whether it is Saddam or someone else."
"I never heard that Saddam Hussein insulted Imam Hussein or Imam Abbas during the investigation," he added.
Efforts to contact Saddam's attorneys were unsuccessful.
On Wednesday night, state-run Iraqiya television quoted unidentified people close to the investigative judges in reporting that Saddam had been assaulted. It reported that Saddam had insulted Imam Hussein and his brother Imam Abbas, two Shiite saints, provoking two of the court's clerks. The station did not say when the alleged incident occurred.
Saddam's lawyers said in July that their client was attacked during an interrogation session. The chief investigative judge of the special court dealing with Saddam denied the claims at the time.
Al-Mousawi said the only incident he was aware of involved court guards.
"Some two months ago, when the investigative judge ended his work, Saddam remained sitting on his chair then started using the place as a podium for political statements. This happened when he saw a camera shooting him," he said.
The judge told Saddam that his comments had nothing to do with the questioning and "at that point two policemen held him, took him from the chair and took him outside the room."