Egypt's prosecutor's office has ordered the arrest of the Muslim Brotherhood leader Mohamed Badie on charges of inciting violence outside the Republican Guard headquarters where 51 people were killed, state news agency MENA has reported.
Other senior Brotherhood officials were also ordered on Wednesday to be detained, including Badie's deputy Mahmoud Ezzat and party leaders Essam El-Erian and Mohamed el-Beltagy.
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One day earlier, Egypt's prosecutor general began investigating 650 people suspected of involvement in Monday's violence, although it did not say who, exactly, was under investigation.
Al Jazeera's Rawya Rageh, reporting from Cairo, said nine others were included in the arrest warrant.
The Muslim Brotherhood has called for an "uprising" to restore President Mohamed Morsi after Monday's shootings.
Thousands of Brotherhood followers have been maintaining a vigil near a mosque in northeast Cairo demanding the reinstatement of Morsi, deposed last week in a coup.
Rageh said that the leaders who had arrest warrants against them were then present at the vigil at Rabaa al-Adaweya mosque in northeast Cairo and that it would be difficult for the police to enter the large crowd of pro-Morsi supporters.
Cabinet offer rejected
The Muslim Brotherhood on Wednesday also rejected an offer to join Egypt's transitional cabinet, as new interim Prime Minister Hazem el-Beblawi announced he would start work on forming an interim government once he met liberal leaders.
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Beblawi told the Reuters news agency that he accepted that it would be difficult to win the unanimous support of Egyptians for his new government.
"Of course we respect the public opinion and we try to comply with the expectation of the people, but there is always a time of choice, there is more than one alternative, you cannot satisfy all of the people," he said.
A spokesman for interim President Adly Manousr, said on Wednesday night that the new government should be formed within the next four days.
Meanwhile, Egypt's main liberal coalition, the National Salvation Front, withdrew its earlier statement rejecting the transition plan for interim rule and issued a statement containing milder criticism, Reuters said.
Beblawi, a liberal economist and a former finance minister, was named the new prime minister on Tuesday.
Liberal opposition chief and Nobel Peace laureate Mohamed ElBaradei was also named vice president and head of foreign relations.
The appointments were followed by an announcement that ministerial posts in the new government would be offered to members of the Freedom and Justice Party, the Muslim Brotherhood's political arm, and to the Al-Nour Party.
Our correspondent Rawya Rageh said that some of the opposition groups such as Tamarrod said that they were not consulted, and that the plans for the interim government was a rushed political process done secretly.
Also on Wednesday, the country's new prosecutor general, Hisham Barakat, was sworn in by Mansour.
The administration decisions come almost a week after the military overthrew Morsi and chose chief justice Adly Mansour to head the Arab world's most populous country.
ElBaradei was initially tipped to lead the cabinet but his nomination was rejected by al-Nour party. The head of the party added that it was still studying ElBaradei's appointment as vice president.
Beblawi now faces the difficult task of trying to reunite a deeply divided country and rescue its battered economy.
Shortly after the Islamist parties made their statements, Egypt's army chief went on state media to say that the military will not accept political "manoeuvring".
Defence Minister Abdel-Fattah el-Sissi said that "the future of the nation is too important and sacred for maneuvers or hindrance, whatever the justifications".
The blueprint unveiled by Mansour is intended to replace the controversial Islamist-drafted constitution which he suspended after last week's coup.
A committee will be set up to make final improvements to the draft before it is put to a referendum.
Parliamentary elections will then follow within three months and Mansour will announce a date for a presidential election once the new parliament has convened.