Mohamed Badie, 70, was detained on Tuesday at a residential flat in NasrCity in northeast Cairo.
A pro-military satellite channel aired footage showing Badie’s detention. According to the channel Badie was on his way to prison under tight security.
Badie and his powerful deputy Khairat el-Shater, who is in custody, will go ontrial later this month for their alleged role in the killing of eight protesters outside the Brotherhood's Cairo headquarters in June.
Al Jazeera reported that Badie had been seen in public only once since Morsi was overthrown and that, with his arrest, most of the Brotherhood's leadership are now in the custody of the military-led government.
A son of Badie was killed in Cairo during last week's "Day of Rage" protests against the army-backed government and the crackdown on its opponents. Ammar Badie, 38, died of a bullet wound sustained while taking part in protests in the city's Ramses Square.
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