Munqidh Al Faraun, the chief prosecutor, argued on Wednesday that Abdullah al-Amiri, the trial judge, was too lenient with defendants who had threatened lawyers and witnesses.
"You allowed this court to become a political podium for the defendants," Munqidh told al-Amiri. "The chief prosecutor's office requests the judge step down from this case."
The request follows witness accounts by Kurds on Tuesday, who told of crimes committed by the deposed government of Saddam two decades ago.
Saddam and six other former aides face genocide and other charges over the Anfal campaign of 1987-88, in which prosecutors say 182,000 Kurds were slaughtered.
Al-Amiri dismissed the prosecutor's demand, saying: "The judge should co-ordinate and make peace so nobody takes advantage of his fairness ... . I have been working in the judicial system for the past 25 years."
During the trial, Saddam has often threatened the prosecutor and argued against witnesses.
Munqidh Al Faraun alleged that al-Amiri was giving the former president time to make irrelevant "political" statements.
"For instance yesterday, instead of taking legal action [against Hussein], you asked his permission to talk," he said.
"The action of the court leans toward the defendants."
An unidentified Kurdish civil attorney also told the court that Saddam "hurt our feelings" in his recent statements at the trial.
"His statements are illegal and must be stopped," she said.
Saddam was uncharacteristically quiet on Wednesday and followed proceedings while holding a Quran.
The judge adjourned the court until Thursday after listening to four witnesses recount how their villages were gassed or how the remains of their relatives appeared in mass graves far away from their homes.
Salah Gader Mohammed Ameen broke down in tears as he told the court how the identity cards of his mother and brother, who disappeared along with his father and another brother, were found in a mass grave 230km away from their village.
"I was only 10 years old when I lost my mum and dad. Nobody can compensate me," he said.
Omer Othmam Mahommed, a former peshmerga fighter, said warplanes bombed mountains with chemical weapons: "I saw some 2,000 to 3,000 sheep dead. The shepherd also died in the attack."
If convicted of genocide and other crimes, Saddam and his co-defendants could face death by hanging.