"Khairat al-Shater and his brother have been arrested at the request of the prosecution," the general, who spoke on condition of anonymity, said on Friday.

Shater, a wealthy businessman seen as the movement's main political strategist, was arrested at his apartment in Cairo.

Security sources said that he was taken into custody on suspicion of incitement to violence.

On Friday, dozens of people were killed and hundreds of others injured across Egypt during clashes between tens of thousands of opponents and supporters of ousted President Mohamed Morsi, according to Egyptian Health Ministry officials.

Earlier in the day, Muslim Brotherhood supreme leader Mohammed Badie said the military involvement against Egypt’s first democratically elected president is illegal and millions will remain on the street until Morsi is reinstated as president.

On Wednesday, Egypt's army chief ousted Morsi, who took office in June 2012, and dissolved the country's constitution in a move aimed at resolving the country’s political crisis.

General Abdel Fattah al-Sisi also said that new parliamentary elections will be held, and declared head of Supreme Constitutional Court Adli Mansour as the caretaker leader.