Judge Mustafa Hassan Abdullah announced his decision to recuse himself minutes after the retrial opened at a Police Academy on the outskirts of Cairo, citing "embarrassment" over the proceedings, according to state-run news agency MENA.
Abdullah said he referred the case to the Court of Appeal amid shouting in the courtroom, where the 84-year-old former dictator had earlier been flown in by a helicopter to face the retrial over the charges linked to nearly 900 protesters' death during the 2011 uprising against his 29-year-old regime.
The judge "submitted a medical report to the head of Cairo Cassation Court stating that he has medical problems with his eyes," Mubarak's lawyer Farid El Deeb was quoted as saying in the media.
Egyptian law requires a judge to recuse himself publicly.
Abdullah was presiding over the retrial of Mubarak, his two sons Alaa and Gamal, fugitive businessman Hussein Salem, ex-interior minister Habib el-Adli and six of his top aides.
Mubarak's earlier trial ended in early June 2012, where he was sentenced to 25 years in prison, the maximum amount of jail time in Egypt. The former president challenged the ruling, and the courts granted him a retrial.
Mubarak, who was toppled in January 2011 during the Arab Spring uprising, has suffered several health scares and MENA even reported him clinically dead at one point.
His two sons are facing trial on corruption charges. His former interior minister 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.
Business tycoon Salem is being tried in absentia.
Mubarak's initial trial in August 2011 was a big moment for the country and the region because it was the first time an Arab leader deposed by his people appeared personally in court. But the drama of those first days, which saw an ailing Mubarak wheeled into court on a stretcher, has since fizzled.
In January, Egypt's highest court the Court of Cassation ordered a retrial for Mubarak after accepting an appeal against his life sentence, citing procedural failings. He is currently being treated at a military hospital in Cairo.
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