(Ahlul Bayt News Agency) - Mr Badie is accused of inciting the violence in Cairo on Monday in which at least 51 people were killed.
Several leading Brotherhood figures are already in detention and warrants have been issued for hundreds more.
It comes as the interim prime minister attempts to form a government after the overthrow of President Mohammed Morsi.
The Muslim Brotherhood, which Mr Morsi comes from, say his ousting by the army amounts to a coup.
Its supporters have been staging large protests at the Rabaa al-Adawiya mosque in the capital, demanding his release from detention and reinstatement.
The movement's political wing, the Freedom and Justice Party (FJP), has said it will not accept an offer to join the cabinet being set up by Prime Minister Hazem al-Beblawi.
Spokesman Gehad El-Haddad told Reuters the charges against Mr Badie and other senior leaders were "nothing more than an attempt by the police state to dismantle the Rabaa protest".
He said some of those wanted by the authorities were at the protest.
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