Brotherhood Supreme Guide Mohamed Badie, 70, and the others were being tried in the same court in Minya Province that condemned 529 members of the Islamist group to death, in what rights groups said was the biggest mass death sentence handed out in Egypt's modern history.
Protests erupted after yesterday's trial began, with police firing teargas to deter hundreds of demonstrators.
The UN human rights office said the mass death sentences contravened international law.
The EU and US also criticised the ruling, as did rights groups.
Nicholas Piachaud, a campaigner at Amnesty International, said: "Yesterday was a death sentence for the credibility and independence of Egypt's criminal justice system.
"There is little hope of the 683 people indicted in this latest trial of receiving fair proceedings before the same judge who yesterday handed down death sentences so readily."
Justice Ministry official Abdel Atheem al-Ashari defended the death sentences, saying in a statement in response to the ruling that the separation between the state and the judiciary was one of the main principles of any democratic system.
There are no signs western powers will back their dismay with action to push for greater democracy in Egypt, which is of strategic importance because of its peace treaty with Israel and contains the Suez Canal, a global shipping lane.
Egypt has cracked down hard on the Brotherhood since army chief Field Marshal Abdel Fattah al-Sisi toppled Mursi, Egypt's first freely elected president, in July, and installed a government.
In August, security forces killed hundreds of Brotherhood supporters who staged a long sit-in to demand Mr Mursi's reinstatement. Thousands of others were arrested and top leaders, including Mursi himself, are also on trial.
Defence lawyers boycotted yesterday's court session - attended by 60 of the defendants - after complaining of irregularities, while journalists were barred from the courtroom.