Judge Raid Juhi, who investigated the toppled Iraqi leader before his trial started, said the resignation of Rizgar Mohammed Amin had not yet been officially accepted, but his role was expected to be filled by Saad al-Hamash, the second-ranking judge trying the case.
Juhi said the law governing the court set up to try Saddam and seven co-defendants prescribed that if the chief judge was to be replaced, his position should be taken over by his deputy.
"I think al-Hamash will take over temporarily until he is appointed through an official notice, but the resignation of Rizgar [Amin] has not been officially accepted and if he changes his mind, he will be back in his post," Juhi said.
The tribunal overseeing the Saddam investigations said Amin wanted to quit for "personal reasons" and not because of government pressure, but his resignation would not prevent the trial resuming on 24 January as scheduled.
Amin became fed up with criticism that he let the proceedings spin out of control, a court official said on Saturday.
Saddam has often grabbed the spotlight during the trial, which has now run for nearly three months, railing at Amin, refusing to show up at one session, claiming that he was tortured and praying in court when the judge would not allow a recess.
Saddam and the other defendants are charged over the death of more than 140 Shia Muslims from the town of Dujail who were killed in retaliation for a 1982 assassination attempt on Saddam. Conviction could bring a death sentence by hanging.