A 16-minute audiotape of Zawahiri released on jihadist forums focused on his native Egypt, where he said military-backed authorities were waging war on Islam at the behest of Israel and the United States.
On July 3, Egypt's military overthrew the country's first freely elected president, the Islamist Mohamed Morsi, following massive protests against his year-long rule.
Morsi hailed from the moderate Muslim Brotherhood, an Islamist group that has long been at odds with the more radical Al-Qaeda, which rejects any participation in democratic elections.
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Zawahiri said the increasingly violent conflict between Morsi's Islamist backers and security forces was a "conflict against Islam, a conflict against sharia (Islamic law), a conflict against admitting the right of the Lord ... in legislation," according to a translation by the US-based SITE Monitoring Service.
He called on Egyptian Muslims to "rid Egypt of this criminal gang that jumped on power with iron and fire and took advantage of the concessions of some factions in their drooling behind the mirage of the delusional reconciliation," in an apparent reference to the Brotherhood.
Zawahiri said the same "tragedy" was unfolding in Tunisia, where the ruling Ennahda, another moderate Islamist party, has agreed to hand power over to a government of independents following a months-long crisis sparked by an opposition MP's assassination.
Having taken over the leadership of Al-Qaeda after Osama bin Laden was killed in a US commando raid in Pakistan in May 2011, Zawahiri is believed to be hiding out in Afghanistan or Pakistan.