The general prosecutor's office said in a statement that it issued arrest warrants for the general guide of the Muslim Brotherhood, Mohammed Badie, as well as for his deputy Mahmoud Ezzat.
Eight other top Brotherhood leaders wanted by the prosecution, included Mohammed al-Beltagui, Mahmud Ezzat and Safwat Hegazi, the sources said.
Badie is accused of inciting the violence in Cairo on Monday in which at least 55 people were killed.
The public prosecutor also charged 200 people held over the bloodshed outside the military barracks, sources said.
Several leading Brotherhood figures are already in detention and warrants have been issued for hundreds more.
Meanwhile, a foreign ministry spokesman told reporters that Egypt's ousted president Morsi is in a "safe place" following his overthrow by the army.
He added that no charges had been levelled against Morsi yet.
"Morsi is in a safe place, for his safety and he is being treated with dignity," Badr Abdelatty told reporters, in the first public statement on the whereabouts of the 61-year-old leader who was ousted by the army last week.
"He is not charged with anything up till now," he said.
Egypt's military-backed interim government was faced with tough hurdles as both opponents and supporters of ousted president Morsi slammed a temporary charter that seeks to steer the divided nation through a rocky transition phase.
Uncertainty ruled in Egypt today as the Muslim holy month of Ramadan began and the military said it would address the issues of this week's deadly violence.
Clashes on Monday between Morsi's supporters and security forces killed 55 people and wounded another 435. It was the deadliest day in Cairo since the revolution that forced former President Hosni Mubarak from office in 2011.
Nearly 650 people, mostly backers of Morsi, were also detained as they tried to storm the Republican Guard headquarters here, where the ousted leader is reportedly under house arrest.
The army, in a statement on the clashes, said, "an armed terrorist group tried to storm" the Republican Guard compound and soldiers retaliated by firing.
Muslim Brotherhood, which has led demonstrations against last week's military overthrow of Morsi, called for an "uprising" and accused troops and police of "massacring" its supporters.
New interim Prime Minister Hazem el-Beblawi announced that he would start work on forming an interim government once he meets with liberal leaders.
Beblawi is expected to offer posts to Morsi's Islamist Muslim Brotherhood, although it has refused to co-operate with what it says is a coup.
Late on Yuesday Ahmed el-Musalamani, spokesman for the interim president, said talks on a new cabinet would start on Wednesday.
He said posts would be offered to the FJP, which won Egypt's first free elections in 2012, and to the ultraconservative Salafist Nour party.
Muslim Brotherhood has outrightly rejected being part of the cabinet, with Mohamed Kamal, a senior official in the Brotherhood's political wing the Freedom and Justice Party, was quoted by the BBC as saying, "We will never take part in any cabinet as long as Morsi is not back as a president."
Violence continued to plague the deeply divided nation as two people were killed and six injured when unknown assailants attacked a security checkpoint in North Sinai late last night, state news agency MENA reported.
Egypt's interim President unveiled a roadmap yesterday for fresh polls by early next year to end the raging political turmoil in the country.
Egypt's interim President Adly Mansour issued the constitutional declaration late Monday night giving himself limited power to make laws, and outlined the timetable for parliamentary and presidential elections.
The whole process will take no more than 210 days, according to the decree, meaning elections will be by February at the latest.
Essam el-Erian, a senior Brotherhood leader, yesterday rejected the transition plan, saying it takes the Arab nation "back to zero."
The liberal National Salvation Front said it was not consulted on the decree and wants changes to be made.
Even the Tamarod movement, which led the mass protests that ousted Morsi, said it had not been consulted on the election plan and was asking to see the interim leader to discuss the situation.