He said Mohammed al-Zawahri, leader of the ultraconservative Jihadi Salafist group, was detained at a checkpoint in Giza, the city across the Nile from Cairo.
Mohammed al-Zawahri's group espouses a hard-line ideology but was not clandestine prior to Egypt's July 3 coup. 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. He spoke anonymously as he was not authorized to talk to the press.
Authorities said earlier that al-Zawahri had commanded insurgents in Sinai Peninsula.
Street fighting in Cairo and other clashes across the country left 173 people dead on Friday, authorities say.
An anti-military coalition led by Morsi's Muslim Brotherhood has called for a week of protests, further escalating unrest in the country. The coalition says that they won't back down until it topples the government installed by the military.
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