Khalil al-Dulaimi, who has been boycotting the genocide trial since the previous judge was sacked by the government in September, made a brief appearance in the Baghdad courtroom on Monday to present a list of 12 requests.
The lawyer called for an investigation into allegations that one of Saddam's co-defendants was beaten by his prison guards last month, and allegations that documents went missing from an office in the Green Zone.
Al-Dulaimi also demanded that the defence counsel be allowed to have Arab and foreign lawyers in court.
Mohammed al-Ureybi, the chief judge, said Arab and foreign lawyers could only attend the trial as advisers. Al-Dulaimi then walked out of courtroom, and the proceedings continued with a court-appointed lawyer.
Before al-Dulaimi made his demands, the judge interrupted him for addressing Saddam as "my president".
The judge said: "There is no president in this court except for the president of this court."
"There is no law that prevents me from calling my president as my president. The defence team insist on calling him [Saddam] as the president"
Khalil al-Dulaimi, Saddam Hussein's chief defence lawyer
Al-Dulaimi said: "There is no law that prevents me from calling my president as my president. The defence team insist on calling him as the president."
Saddam, his cousin Hasan al-Majid, and five other Iraqi commanders are on trial over their alleged roles in the 1988 Anfal (Spoil of war) campaign against ethnic Kurds in northern Iraq which the prosecutuion says killed 180,000 people.
In Monday's testimony, Jamal Sulaiman Qadir, described how "doomsday" came to his village on May 18, 1988 when four warplanes dropped chemical bombs on it. He said when he entered he could see about 20 bodies, including some of his relatives, lying on the ground.
"That day was like doomsday. I could hear children crying for their father and women crying for their husbands ... The bodies were piled up. Some belonged to children who were still clutching lollipops or Eid sweets because it was the last day of Ramadan.
"Saddam had given them Eid presents," he said angrily, adding that his eyes watered and turned red as he carried wounded people away from the area.
Qadir showed the court a list of 35 dead people from his and nearby villages. He told the judge that on August 10, after he had returned to the village, government forces attacked again.
Another witness, Fakhir Ali Hussein, described aircraft coming from Arbil and bombing Banisan, Khatye and other villages.
"Minutes after the bombing, there was a smell in the village ... like rotten apples ... Because of the smell people could hardly breathe and started vomiting. Two people who walked near where one bomb fell had their skin swollen and burnt," he said.
Al-Dulaimi has said that if Saddam is condemned to death in a separate trial, where he is charged with killing nearly 150 people from the village of Dujail, it could provoke civil war in Iraq and unrest throughout the Middle East.
The verdict in the Dujail trial is expected on November 5.
Saddam and seven others are charged with crimes against humanity for the killing of 148 Muslim Shia after an attempt to assassinate him in the village in 1982.