There were chaotic scenes as the judge said he was referring the trial to another court.
Hosni Mubarak was convicted in June 2012 of conspiring to kill protesters during the 2011 revolt that ended his rule.
The former president was sentenced to life but a retrial was ordered in January after he appealed against the sentence.
About 850 people were killed in the 2011 crackdown.
Judge Mustafa Hassan Abdullah announced his decision at the start of the retrial at a police academy on the outskirts of Cairo.
Amid shouting in the courtroom – delaying the start of proceedings – the judge said he was referring the case to the Cairo appeals court as he felt “unease” in reviewing the case, Reuters news agency reported.
That court is then expected to appoint a new panel to hear the retrial.
Hosni Mubarak, 84, is in poor health and currently being held in a military hospital in Cairo.
On Saturday, he was flown by helicopter to the courthouse at a police academy on the outskirts of Cairo.
State TV showed Hosni Mubarak being wheeled into the building on a stretcher, wearing a white outfit. Wearing dark glasses and with an intravenous cannula on his hand, he later waved to the courtroom from inside a cage.
His first trial, at which he also appeared on a stretcher, lasted 10 months.
Two sons of the former leader, former interior minister Habib al-Adly and six aides will also be re-tried, facing the same charges as before.
Habib al-Adly was sentenced to life last year for contributing to the killing of protesters, and for five and 12 years for corruption charges.
Hosni Mubarak’s sons, Gamal and Alaa, will be retried on corruption charges for which they were acquitted in June, because of the expiry of a statute of limitations.
The former leader was also found not guilty of corruption.
Businessman Hussein Salem, a close associated of Hosni Mubarak, is being retried in his absence – he went to Spain after being cleared of fraud in his first trial.
The 18-day uprising in 2011 ended Hosni Mubarak’s 29-year rule of Egypt.
Families of protesters who died in the crackdown were disappointed that the former leader was not convicted of ordering the killings.
There was also been anger among some that he has not faced trial for abuses allegedly committed earlier in his rule.
News of the retrial has been overshadowed by the political instability and insecurity which followed the revolution.
Deaths during the uprising were largely blamed on the police at the time, but last week a report was leaked which implicated the army in serious human rights abuses at the time, including the killing and torture of protesters.
The leaked chapter, reportedly presented to President Mohamed Morsi late last year, contains testimony relating to civilians detained at military checkpoints who were never seen again and reports that the army delivered unidentified bodies to coroners.
Egypt’s Defence Minister Abdel Fatah al-Sissi denied the accusations, calling them a betrayal.
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