The first session Monday saw Morsi and 14 co-defendants in a cage, chanting the trial was illegal inside the courtroom as fighting broke out between supporters and opponents of the deposed president on the streets, Ahram Online reported.
Morsi, ousted by the army July 3 amid huge protests against him, and four other senior Islamists and Muslim Brotherhood officials are standing trial on charges of inciting violence and murder at the Heliopolis presidential palace clashes in December 2012. At least 11 people died and 600 were injured.
The dead and injured were among the tens of thousands who rallied outside the palace gates to protest Morsi's decree granting himself unchecked power to help push through a new Constitution written by Islamists.
Morsi maintains he is Egypt's legitimate president, urging the court "not to provide cover for the criminal coup d'etat" against him.
He said he was brought to court "by force," calling on the judges to allow him to exercise his presidential authority, al-Ahram reported.
Seven of the defendants remained at large and will be tried in absentia, including Islamist activist Ahmed El-Mogheer and cleric Wagdi Ghoneim.
In Alexandria, supporters and opponents of the deposed president clashed, throwing stones at each others, resulting in several injuries and 18 arrests, police said.
Morsi supporters staged demonstrations throughout Egypt to protest the trial.
Ayman Nihad, a lawyer representing 14 defendants, told Ahram Online he wanted access to all documents after the court denied lawyers permission to examine evidence before the trial began.
Among the defense attorneys who were at Monday's hearing was Mohamed Selim el-Awa who said many of Morsi's lawyers weren't being admitted to court, Ahram Online said. Muslim Brotherhood's Freedom and Justice Party website indicated only four of Morsi's 28 lawyers were allowed in court.
"This did not happen during [deposed President Hosni] Mubarak's trial," el-Awa told reporters outside the court.
Families of Muslim Brotherhood loyalists killed during the December clashes released a statement Monday, demanding the "real perpetrators" be brought to justice.
The statement, published on the Brotherhood's Freedom and Justice Party website, said family members of slain Brotherhood follower Mohamed Ibrahim sued former Interior Minister Ahmed Gamal Eddin, National Salvation Front members Hamdeen Sabbahi and Amr Moussa, and newscaster Wael el-Ebrashy, saying they were responsible for the December 2012 clashes at the presidential palace.
U.S. Secretary of State John Kerry said in Cairo Sunday he saw "indications" Egypt was moving back to democracy.
"The road map is being carried out to the best of our perception," Kerry said, referring to the military-led government's plan to hold a national referendum on an amended Constitution and have parliamentary and presidential elections by in the spring.
"There are questions we have here and there about one thing or another," Kerry added in a joint news conference with Egyptian Foreign Minister Nabil Fahmy.
"I think it's important for all of us, until proven otherwise, to accept that this is the track Egypt is on and to work to help it to be able to achieve that," he said.
Kerry downplayed the Obama administration's October decision to suspended the delivery of major weapons systems and withhold $260 million in support for the Egyptian budget.
That was not "punishment" for Morsi's overthrow but rather "a reflection of policy in the United States under our law," he said.
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