The Muslim Brotherhood's spiritual leader was arrested early Tuesday in Cairo's Nasr City district, an Egyptian Interior Ministry spokesman told Efe.
Mohammed Badie was detained along with fellow Muslim Brotherhood member Talat Youssef at an apartment near the plaza where Islamists camped out until police moved in last Wednesday and cleared them out.
Special forces and security service personnel made the arrests after confirming that Badie was in the building.
The Muslim Brotherhood said it named Mahmoud Ezzat to be its interim spiritual leader, Egyptian television reported.
The National Alliance for the Defense of Legitimacy, meanwhile, called for a civil disobedience campaign against the "coup leaders" who deposed President Mohammed Morsi last month.
The alliance, a group of Islamist parties, said it would continue its "peaceful" acts in support of the ousted president.
A boycott of media outlets and companies that supported the coup will be staged, leaders of the alliance, which includes the Muslim Brotherhood, said in a press conference.
Egypt has been locked in a spiral of bloodshed since the security forces moved last Wednesday to break up the sit-in protests staged in Cairo by Morsi supporters.
Morsi's supporters have held protests in Cairo since his ouster by the armed forces in a July 3 coup, which followed days of massive anti-government protests.
Critics accused Morsi and the Brotherhood of doing little to address poverty and Egypt's struggling economy, of failing to advance the goals of the 2011 revolution that forced out strongman Hosni Mubarak and of seeking to monopolize power. EFE