Egypt’s state prosecutor has issued an arrest warrant for Mohamed Badie, the leader of the Muslim Brotherhood, and at least nine other senior figures.
Mohamed Badie is accused of inciting the violence in Cairo on Monday in which more than 50 people were killed.
Many Brotherhood members are already in detention and warrants are said to have been issued for hundreds more.
Meanwhile, a foreign ministry spokesman has said ousted President Mohamed Morsi is being held in a “safe place”.
Badr Abdul Atti told reporters he did not know where the 61 year old was, but that he was being treated in a “very dignified manner”.
“For his own safety and for the safety of the country, it is better to keep him in a safe place. Otherwise, the consequences will be dire,” he added.
Badr Abdul Atti is reported to have denied that Mohamed Morsi was being detained at the Presidential Guard barracks in Cairo, as many believe.
The Muslim Brotherhood, to which he belongs, says his ousting by the military a week ago amounted to a coup.
Its supporters have since been staging protests outside the capital’s Rabaa al-Adawiya mosque, not far from the barracks, demanding his release and reinstatement.
The movement’s political wing, the Freedom and Justice Party (FJP), has said it will not accept an offer to join the cabinet being set up by interim Prime Minister Hazem al-Beblawi, a 76-year-old economist and former finance minister who was appointed on Tuesday.
The arrest warrants could scupper any attempts to persuade the Brotherhood to participate in the transitional political process.
Spokesman Gehad el-Haddad said the charges against Mohamed Badie, known as the General Guide, and other senior leaders, were “nothing more than an attempt by the police state to dismantle the Rabaa protest”.
Prosecutors also said they had ordered 200 people – believed to be Brotherhood members – to be held in custody for at least 15 days pending further investigation into accusations of murder, incitement to violence, carrying unlicensed weapons and disrupting public order. Another 450 have been released on bail.
There were conflicting reports about what happened on Monday, with the interim authorities being accused of a cover-up.
The Brotherhood maintains that soldiers carried out a massacre of peaceful demonstrators, who had been taking part in dawn prayers outside the Presidential Guard barracks.
But the police and the military say they acted in self-defence, and had opened fire only after being attacked by armed assailants.
More than 50 Brotherhood supporters were killed, as well as a soldier and two policemen.
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