But the move is unlikely to halt the trial, Saddam's second, since the chief judge said he would appoint replacements after the lawyers stormed out of court last week.
The move could raise further doubts, though, about the court's legitimacy - already under fire following the replacement of the chief judge who had been criticised for allegedly favouring the defence.
Saddam's head lawyer, Khalil al-Dulaimi, called the decision to replace Judge Abdullah al-Amiri a "flagrant violation of the law" because it was "dictated by the government and not the court".
Al-Dulaimi also accused the five-judge panel of committing "several violations of the law", including refusing to hear non-Iraqi lawyers and requiring foreign attorneys to seek permission to enter the courtroom.
Among Saddam's nine lawyers are a Jordanian, a Spaniard, a Frenchman and two Americans, including former US attorney general Ramsey Clark.
"We will not just sit there gagged to give it legitimacy," said Mr al-Dulaimi, an Iraqi. But softening his tone somewhat, he said he hopes "the court will listen to our requests and that's when we'll go back to the courtroom".
Saddam and seven others have been on trial since August 21 for a crackdown on Kurdish guerrillas in the late 1980s.
The prosecution claims about 180,000 people, mostly civilians, died in attacks that included the use of poison gas against Kurdish towns and villages in northern Iraq.
The defence also boycotted the final stages of Saddam's first trial, for his alleged role in the deaths of 148 Shiite Muslims in Dujail, following an assassination attempt against him there.
A verdict in that trial, which began October 19, 2005, is expected when the court reconvenes next month. Saddam and his seven co-defendants could receive the death sentence if convicted.
On Tuesday, the government said Iraqi Prime Minister Nouri al-Maliki approved a request by the Iraqi High Tribunal to remove al-Amiri, replacing him with his deputy Mohammed Oreibi al-Khalifa.
Al-Amiri had angered Kurdish politicians by declaring in court that Saddam was "not a dictator".
Al-Dulaimi has now questioned the legal qualifications of the new chief judge.
"He lacks the experience and the calibre needed in this trial," he said.
The change in the chief judge also drew criticism from the US-based organisation Human Rights Watch, which said al-Amiri's removal "appears to be improper interference in the independence of the tribunal".