Even if Rizkar Mohammed Amin's decision to step down is accepted, it will not affect the trial of Saddam and seven former aides, which is due to resume on January 24, the Iraqi High Tribunal added.
Judge Amin tendered his resignation more than five days ago, deciding to quit "for personal reasons, and not because of government pressure," the tribunal confirmed in a statement.
"The cabinet has not yet ruled on his resignation," it said.
If his resignation is finalised, Judge Amin would be the second judge on the five-strong panel trying Saddam to quit since hearings began in a high-security courtroom in Baghdad's Green Zone on October 19.
A top Iraqi diplomat in the United States suggested, however, that Judge Amin would only resign as the presiding judge and remain on the five-strong panel of judges trying the case.
"He would be stepping down, as I understand it, as presiding judge, not as a judge of the court not and not even as judge in this case," Feisal al-Istrabadi, Iraq's deputy UN representative, told CNN television.
Under pressure
Judge Amin has come under pressure for allowing what critics see as theatrics by the defence counsels and by the accused during just seven courtroom days.
His supporters say the judge has sought to give the defendants, who face a possible death penalty, as much leeway as possible in a bid to ensure the process is seen as fair.
An official close to the court said efforts were under way to try to get Judge Amin to change his mind.
Judge Amin, a Kurd, is the only judge in the Saddam trial who has allowed himself to be identified in court. The other four remain anonymous for fear of reprisals for taking part in the case.
Two defence lawyers were shot dead shortly after the opening of the trial.
Saddam's leading counsel Khalil al-Dulaimi welcomed the resingation news, but said it made no difference to the case as the defence team considered the court illegal.
A spokeswoman for the office of Prime Minister Ibrahim Jaafari confirmed that his chief of staff received Amin's letter of resignation a few days ago.
Mr Jaafari himself was out of Baghdad, however, visiting Al-Anbar province, a restive Sunni stronghold to the west of the country, with General George Casey, the top US commander in Iraq, and US ambassador Zalmay Khalilzad.
The prime minister, a Shiite, announced on television that the government would give 75 million dollars to the province for reconstruction projects.
Detainees freed
In other developments, the US military freed 509 Iraqi detainees from three prisons, including two journalists who work for Reuters, the justice ministry and the British news agency said.
US-led forces are still holding more than 14,000 Iraqis in prisons across the country on suspicion of taking part in the insurgency.
On the election front, Iraq's electoral commmission will reveal the outcome of an investigation on Monday into a raft of complaints of fraud arising out of last month's parliamentary poll, a spokesman said.
A team of foreign monitors said, for its part, that it will release the conclusion of a separate probe into the election on Thursday.
Initial indications from the December 15 vote showed that Iraq's Shiite majority came out on top, but final results have been delayed by allegations of ballot-rigging from Sunni-backed and secular parties.
It is doubtful that the ultimate certified results will be known before the end of the month because of an appeals period and other technical matters.
In subdued unrest, a police official was shot dead in Baquba, northeast of Baghdad, on Sunday by unknown assailants, a security source said.
In a sign of further violence ahead, six Islamist groups announced on
Sunday the creation of a council to unify their fight against "the crusaders and apostates" in Iraq and urged Muslims to join their struggle.
Meanwhile, four Iraqi civilians and a US soldiers were killed in a car accident in the northern Iraqi city of Mosul on Sunday, the military said.