The list includes leading Brotherhood figures Essam El-Erian and Mohamed El-Beltagi, both of whom were attending a demonstration on Monday, according to the Brotherhood.
They were also included in a similar list last week of people charged with inciting violence, but have not been arrested.
The latest charges accuse them of "inciting violence and funding violent acts.”
Earlier, Egypt's public prosecutor also ordered the arrest of Muslim Brotherhood supreme guide Mohammed Badie and other top leaders of the movement for inciting violence that left dozens dead outside the headquarters of an elite army unit.
At least 51 people were killed in clashes outside the Republican Guard headquarters in Cairo where supporters of ousted president Mohamed Morsi were calling for him to be reinstated.
Other senior Brotherhood officials were also ordered to be held over the violence, including Mr Badie's deputy Mahmoud Ezzat, according to judicial sources.
Prosecutors said that 200 people had been charged altogether over their involvement in the deadly clashes. Mostly Morsi supporters, they will be held for 15 days pending investigation into accusations of murder, incitement to violence, carrying unlicensed weapons and disrupting public order and security.
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