Other defendants have arrived at the police compound by helicopter but Mohamed Morsi is still in Alexandria.
Mohamed Morsi and 14 other Muslim Brotherhood figures are accused of inciting the killing of protesters outside a presidential palace in 2012.
He was removed by the army last July after demonstrations against his rule.
Mohamed Morsi’s supporters have since held regular protests calling for his reinstatement.
Last Friday at least 11 people died in clashes between police and pro-Muslim Brotherhood demonstrators across Egypt.
A helicopter carrying some of the defendants arrived at the National Police Academy complex in Cairo for the hearing early on Wednesday, reporters said.
However state media said Mohamed Morsi’s arrival had been delayed by bad weather. He is being held at the city’s Burj al-Arab prison.
Egyptian media said thousands of police were on alert and TV pictures showed some pro-Morsi protesters being arrested as they waved the four-finger salute adopted by supporters of the ousted president.
Mohamed Morsi is due to be asked to appoint a lawyer, which he refused to do during his initial appearance.
He also faces several other charges ranging from fraud to colluding with foreign militants in a terrorist plot.
Mohamed Morsi faces another court hearing at the end of January, accused with some 130 others of murdering policemen during a mass breakout from a Cairo prison in January 2011 shortly before the overthrow of President Hosni Mubarak.
Human rights groups have dismissed some of the allegations against him as preposterous.
Egyptian officials insist Mohamed Morsi will be given a fair trial but lawyers trying to defend him say they have been denied access to him.
He first appeared in court in early November amid chaotic scenes.
Speaking from behind bars, he insisted he was still the president and was being held against his will.
Mohamed Morsi refused to acknowledge the legitimacy of the court and would not wear a prison uniform.
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