Saddam's lawyers said the confusion showed the court could not give the ousted Iraqi leader a fair trial and was under too much political pressure.
The trial, which was meant to be a landmark in Iraq's political process, has already been marred by delays, the assassinations of two defence lawyers and chaotic courtroom outbursts by Saddam.
Since the trial's last session on December 22, the five-member panel of judges hearing the case has been thrown into confusion.
The chief judge presiding since the trial's start resigned, complaining of criticism from politicians that he was not doing enough to rein in Saddam.
The member of the panel initially named to replace him was suddenly removed, and instead a new chief judge, Rouf Abdel-Rahman, was brought in.
Judges split
After hours of waiting for the start of Tuesday’s court session, court official Raid Juhi told journalists the court had decided to postpone the hearing until Sunday.
He blamed the delay on witnesses who failed to appear because they were performing the hajj pilgrimage to Saudi Arabia, which ended more than a week ago.
But two judges said the real reason was a split among the judges over the naming of Abdel-Rahman to head the panel.
Some judges opposed the appointment, while others supported Abdel-Rahman, one of the two judges said.
The other judge appeared to complain about outside interference in the court. When asked what the problem was, he replied, "Matters are not in our hands".
It appeared some members were trying to bring back the former chief judge, Rizgar Mohammed Amin, or the another jurist who was removed from the panel, Saeed al-Hammash.
The two judges spoke on condition of anonymity since court rules bar most judges from being named.
Saddam's Qatari lawyer Najib al-Nuami, said the reason for the aborted session was that Abdel-Rahman was angry at security measures which led to his being searched.
"When the new judge came to the court he was searched vigorously by the Americans, which he did not like," said Mr Nuami, a former Qatari minister of justice.
Security problems
Security measures are very strict with lawyers, witnesses and journalists carefully vetted and searched at the court. He also said that one of the judges had collapsed.
"One of the judges suffered a high-blood pressure attack and I just saw him in the hospital," Mr Nuami said.
Another defence lawyer, who declined to be named, said he too had heard that the presiding judge had problems with the security arrangements at the court.
Ramsey Clark, a former US attorney-general who has joined the defence team, said political pressures on the court "make it impossible for fairness".
"The court is not independent. It can't function well," Mr Clark told CNN.
Iraq's Shi'ite Muslim leaders have said they want Saddam's trial to be swift.
The case Saddam is being tried on, the killings of about 140 Shi'ites in a crackdown that followed a failed 1982 assassination attempt against Saddam in the village of Dujail, was chosen expressly because officials believed it would be quick case to try.
Saddam and seven co-defendants could face the death penalty.