He said Mohammed al-Zawahiri, leader of the ultraconservative Jihadi Salafist group, was detained at a checkpoint in Giza, the city across the Nile from Cairo.
Mohammed al-Zawahiri's group espouses a hard-line ideology but was not clandestine prior to Egypt's July 3 coup.
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He was allied with ousted President Mohammed Morsi, an Islamist, whose supporters are now taking to the streets to protest the killings of its supporters in a security crackdown last week.
The official declined to give further details.