El-Shater, pictured, is the latest prominent Muslim Brotherhood leader to be taken into custody since Morsi was removed from office by the army earlier this week. He was arrested with his brother in an apartment in eastern Cairo on allegations of inciting violence against protesters, Hani Abdel-Latif, a spokesman for Egypt's Interior Ministry, told the AP news agency.

"Khairat el-Shater and his brother have been arrested at the request of the prosecution," an anonymous general from within the Interior Ministry told the news agency AFP. "They went quietly."

Watch video 01:47 Violence rocks Egypt after coup

El-Shater, the deputy of the Brotherhood's supreme leader, Mohammed Badie, is seen as the party's main political strategist and its most powerful decision maker. The wealthy businessman was the group's original candidate for president but Mohammed Morsi ran instead, with el-Shater disqualified because of a past prison sentence.

Morsi, who came to power as Egypt's first freely elected president a year ago, was overthrown by the military following protests by millions across the country calling for his removal. They had accused him of squandering his electoral mandate by putting power in the hands of hard-line Islamists and failing to deal with a spiraling economic crisis.

Morsi supporters, in turn, accused the military of wrecking Egypt's attempts to install democracy by carrying out a coup against an elected leader.

Badie vows to reinstate Morsi

Muslim Brotherhood leader Mohammed Badie appeared at a huge Cairo rally on Friday, calling for Morsi's reinstatement and vowing that Brotherhood followers would continue their protests, as violence mounted across the country.

Badie also denied reports he had been arrested. Security sources had previously said that Badie was among a number of Muslim Brotherhood leaders arrested in the wake of the military's removal of Morsi.

"All the measures taken are invalid," Badie said at the rally. "The millions supporting Morsi will stay in the squares until the president of Egypt is reinstated."

Deadly clashes in Alexandria

In Egypt's second city of Alexandria, 12 people were killed on Friday in street fighting between supporters and opponents of Morsi. An emergency services official, Amr Salama, told AP that hundreds of Islamists broke into a rally by Morsi opponents, and opened fire with guns. Salama said police joined the side of the opponents.

In Cairo's Tahrir Square, state television reported the deaths of two people, killed when Morsi supporters traded fire with opponents. The official MENA news agency said four protesters were killed outside the Republican Guard headquarters, after they broke away from a pro-Morsi demonstration.

Violence across the country killed at least 26 on Friday.

jr/jm (AP, AFP, Reuters)