Downtown Cairo prosecutor general Hamdy Mansour issued an arrest warrant for Al Jazeera news channel director Abdel Fattah Fayed.
The director faces charges of threatening public peace and national security through broadcasting incendiary news.
Military and Interior Ministry raided the headquarters of Al Jazeera Mubasher Wednesday evening after an army statement in which Defence Minister General Abdel Fattah al-Sisi overthrew President Mohamed Morsy and appointed Supreme Constitutional Court chief Adly Mansour as interim president in his place.
The prosecutor accused Al Jazeera had broadcast material that incited violence.
Prosecutors have also charged Fattah Fayed with operating without a license, in contravention of Egypt's Investment Law.
The channel has been operating without legal offices in Cairo, after being shut down under the former Supreme Council of the Armed Forces (SCAF) regime, the prosecutor added.
Al Jazeera Mubasher managing director, Ayman Gaballah, earlier claimed in statements to prosecutors that the channel in fact possesses the necessary broadcasting licenses. The prosecution have asked to see the relevant documents as proof.
Prosecutors in Agouza decided to release Gaballah yesterday on LE10,000 bail.