Egypt coup: Muslim Brotherhood calls for protests as military arrests leader Mohammed Badie

Arrests of some 12 officials are confirmed but the figure could be three times as high

Fresh from toppling the country's first democratically elected leader, Egypt's military risked further outrage from the Muslim Brotherhood by arresting the group's Supreme Guide as he was staying in a resort by the Mediterranean coast.

Mohammed Badie, the Brotherhood’s spiritual leader, was arrested at an acquaintance’s villa in Mersa Matruh in north-west Egypt. He was then flown to Cairo on a military helicopter, according to security officials.

“This is even worse than it was for us under Hosni Mubarak,” said Amr Darrag, a leading Brotherhood official.

Supporters of the ousted ruling party are expected to rally again today despite Mr Badie’s arrest being part of a wider crackdown against the Brotherhood that saw the authorities issue a wanted list for 200 of its members.

The development came as the military oversaw the swearing-in of Egypt’s interim President just 24 hours after it toppled Mohamed Morsi. Adli Mansour, formerly a leading judge, will preside over a provisional government until elections are held, although no date has yet been set.

Mr Mansour had been one of the candidates put forward by the opposition groups that spearheaded this week’s insurrection against Mr Morsi.

In a ceremony aired live on state television, Mr Mansour said that there would be “no exclusion of anyone” under his rule. As news spread of the anti-Islamist crackdown, he offered an olive branch to the Muslim Brotherhood and said he wanted them integrated into the nation. He added that the 30 June revolt had “corrected the path of the glorious revolution” which took place two and a half years ago.

The prospect of compromise was scotched by the Brotherhood. “We declare our complete rejection of the military coup staged against the elected president and the will of the nation,” it said in a statement.

At least a dozen Brotherhood officials have now been detained, according to one NGO director, although another human rights worker said the number of Islamists arrested could be nearly three times that figure.

Prosecutors also announced that Khairat el-Shater, the leading Brotherhood strategist who almost ran for president in 2012, is wanted for arrest. Meanwhile, Mohamed Morsi is being held with his aides at a military intelligence facility, according to a security source who spoke to Reuters.

Egypt’s state news agency reported that officials issued the warrants for Mr Badie and Mr Shater in connection with the deaths of eight protesters killed during clashes outside the Brotherhood’s headquarters on Sunday.

The crackdown came after authorities moved to silence the Islamist media in the wake of Wednesday’s military coup. Following the dramatic moment that General Abdel Fattah al-Sisi, the head of Egypt’s armed forces, announced the military was taking over, the Muslim Brotherhood’s Misr 25 channel went off air. Other Islamist stations were also cut off and their owners reportedly detained. In addition travel bans have been slapped on Mr Morsi and other leading figures from the Brotherhood.

After the general’s address, clashes between pro- and anti-Morsi factions across Egypt left 10 people dead and more than 400 injured. Security forces rounded up Saad el-Katatni, the former speaker of parliament who was also head of the Brotherhood’s political wing, while a deputy leader of the group, Rashad al-Bayoumi, was also arrested. Both men were reportedly being held at Cairo’s Tora Prison, .

According to Gamal Eid, the director of a leading Cairo NGO, his staff tracked at least 34 cases of Muslim Brotherhood and Islamist figures who have been arrested following the coup. “This makes me worried,” he said. “You can arrest someone if they have done a crime but not just for their political background.”

Another prominent NGO official, who asked to remain anonymous, told The Independent that the arrests of at least 12 Brotherhood officials have been confirmed.

She said they included Essam el-Haddad, the former national security adviser to Mr Morsi, who on Wednesday had added to the unfolding drama by releasing an emotional Facebook statement condemning the coup and warning of further bloodshed. Khaled al-Qazzaz, one of the group’s foreign relations advisers, had also been detained by security forces, she said.

The army has said it would guarantee the right to peaceful protest ahead of more predicted unrest, but fears as to their sincerity remain. In a statement on Facebook on Thursday, army command said it would not take "arbitrary measures against any faction or political current" and would guarantee the right to protest, as long as demonstrations did not threaten national security.

The Brotherhood urged people last night to take part in a "Friday of Rejection" protest following weekly prayers. The call is being seen as a test of whether Mr Morsi still has substantial support in the country.

Some analysts have speculated that the Brotherhood may resort to violence, yet the Islamist group has so far eschewed any outright call for revenge. Deserted almost entirely by its political allies, bereft of its arrested leaders and loathed by millions, it probably feels unable to respond adequately, according to the Egypt expert Nathan Brown. “The Brotherhood is standing alone,” he said. “It’s an organisation which isn’t accepting what’s happening but is not doing anything to resist, apart from complaining.”

Video: Fireworks as Morsi is ousted