The Egyptian prosecutor's office has ordered the arrest of Muslim Brotherhood leader Mohamed Badie on charges of inciting violence, state news agency MENA reported.
The office also ordered the arrest of other senior Brotherhood officials, including Badie's deputy Mahmoud Ezzat and party leaders Essam el-Erian and Mohamed el-Beltagi, it stated.
The charges relate to what Egypt's military described as an "assault" by supporters of ousted president Mohamed Morsi on the Republican Guard headquarters on Monday, which left 55 people dead.
The Muslim Brotherhood said its leaders have yet to be detained.
Spokesman Gehad el-Haddad said the charges were "nothing more than an attempt by the police state to dismantle the Rabaa protest," a vigil being held by its supporters at the Rabaa Adaweya square in northeastern Cairo.
The Muslim Brotherhood tells ITV News they are against violence but will "pay the price of their blood" to restore their ousted president.
Egypt's army has named two further officials in the transitional government as its supporters and opponents vowed to stay on the streets.
There has been outrage in Egypt after 51 people were killed near an barracks where ousted President Mohamed Morsi is thought to be held.