Ali was arrested before leaving the country for Rome, security sources told Anadolu Agency. He shaved his beard in an effort to mislead the airport authorities, but was still identified.
Ali's name was placed on a no-fly list upon a request from a security agency, the sources added, without naming the security body behind the request.
Ali's arrest came one day after the Brotherhood leader, Mohamed Badie, was seized near Rabaa al-Adawiya Square.
He faces charges of incitement to violence in connection with the clashes outside the group's Cairo headquarters earlier this year in which nine people were killed.
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