The former Iraqi leader said in a letter that he was boycotting proceedings because he did not recognise the legitimacy of the court, charging that it was making a mockery of justice.
Other high-profile defendants, including Saddam's half brother and former secret police chief Barzan al-Tikriti and the ex vice president, Taha Yassin Ramadan, were also not in court.
Saddam and his co-defendants are accused of ordering the killing of 148 Shia villagers from Dujail after a botched assassination attempt there against the deposed leader in 1982.
They face execution by hanging if found guilty on charges including murder and torture.
And the chief prosecutor last month recommended that two minor officials, Ali Daeh Ali and Mohammed Azzawi Ali, be released.
But Saddam and his top former aides and their lawyers appear to be boycotting the final phase of the trial, although the court's chief investigative judge, Raed al-Juhi said their action would not delay proceedings.
"The tribunal will continue its sessions today and in the next few days to hear the defence's closing arguments, be it with lawyers appointed by the defendants or those appointed by the court," he told reporters.
"If it is court-appointed lawyers, the tribunal can give them extra time to prepare their arguments."
After the defence arguments for the low-profile defendants, the court is expected to take a two-week break before hearing the defence arguments for Saddam and his close associates.
Saddam's main lawyer, Khalil al-Dulaimi, said from Cairo on Monday that most of the defence team would also boycott the proceedings "until our demands are satisfied".
He said the lawyers wanted protection for themselves and their families to be provided by a "neutral third party", and for their "right to defend to be respected".
Khamis al-Obeidi, a member of Saddam's legal team, was assassinated last month, the third defence lawyer to be killed since the start of the trial in October.
Juhi said the lawyers had declined security measures offered by Iraqi and US-led forces.