The officials say police detained senior Brotherhood leaders Mohammed el-Beltagy, Essam el-Erian, group spokesman Ahmed Aref and its chief theologian Abdel-Rahman el-Bar.
Also captured is top cleric Safwat Hegazy, who is close to the Brotherhood.
El-Beltagy, el-Erian and Hegazy are reportedly wanted by prosecutors to answer allegations of inciting violence and conspiring to kill protesters calling for Morsi’s ouster.
The five were arrested shortly after police completed its control of the camp in Cairo’s eastern Nasr City district.
Riot police backed by armored vehicles, bulldozers and helicopters Wednesday swept away two encampments of supporters of Morsi, sparking running street battles elsewhere in Cairo and other Egyptian cities.
The assault to take control of the two sit-in sites came after days of warnings by the interim administration that replaced Morsi after he was ousted in a July 3 coup.
The camps on opposite sides of the Egyptian capital began in late June to show support for Morsi. Protesters — many from Morsi’s Muslim Brotherhood — have demanded his reinstatement.
The violence drew condemnation from other predominantly Muslim countries, which said the crackdown will only make it more difficult for Egypt to move forward.
NJF/NJF