Thirwat Salah Shehata was arrested in a Cairo suburb, the sources said, adding he had been sentenced to death in absentia in the 1990s for an attempted assassination of a minister.
Shehata is believed to have been a deputy to Zawahiri when he ran the Egyptian Islamic Jihad before joining forces with former Qaeda chief Osama bin Laden, killed by US special forces in 2011.
Shehata was reportedly detained in Iran following the US-led invasion of Afghanistan after the September 11 attacks in 2001, which routed Al-Qaeda and forced its leaders into hiding.
Al-Qaeda inspired militants have killed almost 500 Egyptian policemen and soldiers in attacks since the army toppled Islamist president Mohamed Morsi in July.
