The same court in the southern province of Minya also reversed 492 of 529 death sentences it passed in March, commuting most of those to life in prison.
The court, presided over by judge Said Youssef Sabry, had sparked an international outcry with its initial sentencing last month amid an extensive crackdown on supporters of ousted Islamist president Mohamed Morsi.
Under Egyptian law, death sentences are referred to the top Islamic scholar for an advisory opinion before being ratified. A court may choose to commute the sentences, which can later be challenged at an appeals court.
The judge will confirm the verdict on June 21.
Of the 683 sentenced on Monday, only about 50 are in custody. The others have a right to a retrial if they hand themselves in.
Monday’s hearing lasted just 10 minutes, said Khaled Elkomy, a defence lawyers who was in court.
The verdict was the first against Badie, spiritual head of Morsi’s Muslim Brotherhood, in the several trials he faces on various charges along with Morsi himself and other Brotherhood leaders.
Several female relatives waiting outside the courtroom fainted on hearing news of the verdict.
“Where is the justice?” others chanted.
Some said family members had been unjustly convicted or put on trial.
“My son does not even pray, he does not even know where the mosque is,” said one woman, whose son was among the 529 sentenced to death in March. READ: Egypt court sentences 529 Morsi supporters to death.
Karima Fadl, the mother of a man whose death sentence was commuted, said: “My son Khaled received a life sentence.
“It is not better than a death sentence. It is still an injustice. He did nothing wrong.”
Those sentenced on Monday were accused of involvement in the murder and attempted murder of policemen in Minya province on August 14, the day police killed hundreds of Morsi’s supporters in clashes in Cairo.