Morsi's Islamist allies denounce the prosecutions as show trials and political vengeance. The authorities, meanwhile, seek to show that the Brotherhood has been fueling violence in the country, during Morsi's one-year presidency and after the coup, and to establish legal justification for imprisoning them.
Egypt's deputy prime minister, meanwhile, said on Tuesday that the Muslim Brotherhood must first renounce violence and accept the military-backed roadmap for the country's transition before it can join the political process.
Ziad Bahaa-Eldin's comments, made to a small group of reporters including The Associated Press, were the first definitive word by a senior government official on where things stand between the military-backed authorities and the Muslim Brotherhood.
They pointed to how any talk of "reconciliation" or bringing the Brotherhood back into politics a call repeatedly made by the United States has so far found no resonance on either side. Morsi's allies have rejected the new, military-backed government and have stuck to their demand that he be reinstated in office. They have continued frequent protests, often leading to clashes with security forces that have killed well over 1,000 people. The Brotherhood says its protests are peaceful, but the authorities accuse them of provoking violence.
Bahaa-Eldin, a prominent liberal politician, blamed the Brotherhood for the "continuation of the atmosphere of violence" since Morsi's ouster. The Brotherhood, he said, has "the capacity to control the violence."
He said that, beside renouncing violence and accepting the road map, any talks with the Brotherhood will be part of multilateral negotiations to hammer out a formula for political inclusion, and not government-to-Brotherhood contacts.
"There has not been even a signal from the Muslim Brotherhood that it accepts," he added.
In a show of confidence, Bahaa-Eldin said Egypt's ailing economy can withstand the turmoil even if no resolution is reached with the Brotherhood. "Egypt can live with a level of violence and instability," he said. "The economy will not be crippled and will continue to grow by 2 or 3 percent," said Bahaa-Eldin, who is also foreign cooperation minister.
The judges in Tuesday's trial stepped down from the trial of 35 Brotherhood members, including the group's top leader Mohammed Badie and his powerful deputy Khairat el-Shater, on charges of inciting violence. The move forces the trial, which was only holding its second session Tuesday, to start over.
The move amounted to a sharp criticism of the proceedings. So far, in its two sessions since August, none of the defendants has attended the trial, apparently out of inability to ensure their safety or fear Brotherhood supporters would hold protests outside the Cairo Criminal Court where it is being held.