Muslim Brotherhood leader Mohammed Badie, who was arrested on Tuesday, is to be held for 15 days on allegations of having incited the murder of protesters, Egyptian state television reported.
Badie had been in hiding since July 10 when a warrant was issued for his arrest over accusations he incited the deaths of protesters outside the Brotherhood's Cairo headquarters in late June.
Egypt's authorities have this month rounded up dozens of senior Brotherhood leaders.
Ousted president Mohammed Morsi, who hails from the group, remains held at a secret location and is also accused of inciting the deaths and torture of protesters.
The allegations against Badie, who was arrested with two other Brotherhood members, relate to the deaths of eight protesters outside the group's headquarters.