Raouf Abd al-Rahman, the chief judge, adjourned the trial
on Thursday after hearing the testimony of two witnesses.
The trial resumed earlier on Thursday without any of the eight defendants in court.
Saddam failed to appear for a second day and members of his defence team said they would not return to court unless Abd al-Rahman resigned.
Abd al-Rahman went ahead with the trial, saying: "Because of the insistence of Saddam Hussein, Barzan al-Tikriti, Taha Yassin Ramadan and Awad al-Bander not to attend, the court has decided not to call them for this session and to review their opposition."
He was referring to the former Iraqi president, his half-brother, Iraq's former vice-president and the former head of Saddam's Revolutionary Court.
"The rest were present but were causing chaos," he said, explaining a decision to exclude the remaining three defendants, former low-ranking members of Saddam's Baath party.
The defence team, headed by Khalil al-Dulaimi, has accused Abd al-Rahman of bias and of rushing to hand down a death sentence against the toppled Iraqi leader.
Saddam, four former aides and their legal team had previously boycotted Wednesday's session, throwing into further disarray a trial already marked by angry outbursts from Saddam.
Saddam and his co-defendants are on trial over the killing of 148 men from the Shia town of Dujail after an attempt to assassinate Saddam there in 1982.