Mahmoud Ezzat was appointed as the supreme guide of the group after its spiritual leader Mohammed Badie was arrested as part of a crackdown on Islamists demanding reinstatement of ousted President Mohammed Morsi.
"Mahmoud Ezzat, deputy leader of the Muslim Brotherhood, will assume the role of supreme guide of the group on a temporary basis after the security forces of the bloody military coup arrested supreme guide Mohamed Badie," the Freedom and Justice Party website said.
Badie, 70, the Supreme Guide of the Muslim Brotherhood, was arrested in an apartment close to Rabia al-Adawiya square, where Islamist supporters of Morsi held a vigil before it was cleared in a bloody crackdown by security forces last week.
The detention of Badie could throw the Brotherhood into further disarray as the Islamist group continues to protest the ouster of Morsi by the army on July 3.
A state of emergency is in force amid a crackdown on Islamists opposed to the army's ousting of Morsi and almost 900 people have been killed in the violence.