Dozens of relatives of those killed in Egypt's demonstrations gathered outside the court, state-run Nile TV reported. They were joined by hundreds of pro-Mubarak activists carrying signs of support.
Galal Faisal Ali, whose brother Naser was killed in the uprising, said he fears Mubarak will be found innocent.
"The government is not giving us the moral support we need, and they're allowing this circus of a trial to continue. We were hoping for a death sentence, but the way it's going, we may see Mubarak free, and his sons free, which means my brother died for nothing," he said.
Magdi Fouda, the main organizer of the pro-Mubarak protest, is a member of a group called "We are sorry, Mr. President." She was joined by a second group called "Sons of Mubarak."
"We are sure Mubarak will be pronounced innocent," she said.
State security forces formed a barrier between the opposing protesters.
Emotions ran high at Mubarak's original trial in 2012, resulting in scuffles between the two sides inside the courtroom and rioting outside.
Mubarak's two sons, six of his security aides and his former interior minister, Habib al-Adly, all face trial with him. The other defendants had also appeared at the criminal court inside the academy, state TV reported.
In addition to the charges related to the killings, all face charges of financial corruption and abuse of power.
Like Mubarak, al-Adly was found guilty in the original trial and sentenced to life in prison, but was granted a retrial after filing an appeal.
Prosecutors have added an additional corruption charge that was not part of the original trial. Mubarak is accused of selling natural gas to neighboring Israel for prices below fair market value.
Morsy pleased about second trial
Essam El-Erian, a senior adviser to Egyptian President Mohamed Morsy, said in January that the government looked forward to a second trial.
"God willed the retrial would take place under Morsy's rule, with new evidence and new defendants," El-Erian said.
Mubarak, who ruled Egypt for 30 years with the help of the military, was found guilty in June 2012 of ordering the killing of protesters and was immediately transferred to Tora prison in Cairo to serve his life sentence.
The 84-year-old has suffered a range of physical problems since he was driven from office in 2011, following weeks of protests by Egyptians demanding more freedom and reforms.
In December, Mubarak was transferred to a military hospital after suffering a head injury and a bruised chest when he slipped in a prison hospital bathroom, Egyptian state-run media reported.