The president's spokesman Ahmed el-Musalamani said "Morsi is not a political prisoner" and prosecutors and the judiciary is looking into the charges against him.
In a bid to try and mediate a solution to the crisis, the EU's Ashton has planned meetings with both sides Monday. She met with el-Sissi, Foreign Minister Nabil Fahmy as well as Vice President Mohamed ElBaradei. Her office said in a statement she was also to meet with interim President Adly Mansour.
The Brotherhood's political wing says four of its members and Morsi's ex-prime minister, Hesham Kandil, are holding talks with Ashton as well.
While the Brotherhood and its Islamist allies have rejected the new political order, the military-backed interim leadership is pushing ahead with a fast-track transition plan to return to a democratically elected government by early next year.
In a statement before arriving to Cairo, Ashton said she is going to speak to all sides to reinforce that "there must be a fully inclusive transition process, taking in all political groups, including the Muslim Brotherhood."
"I will also repeat my call to end all violence. I deeply deplore the loss of life," she said.
The Egyptian presidency said the vice president received a call from U.N. Secretary-General Ban-Ki moon Monday urging an end to violence and a roadmap that includes the political participation of all parties.
Divisions between pro and anti-Morsi camps have played out in nearly daily street battles, with a dozen homes catching fire in Cairo late Sunday. Security officials said that no one was injured when the ousted president's supporters threw firebombs from atop a main overpass onto homes and opponents below.
Security officials said Monday that 11 bodies with signs of torture have been found in areas around the two pro-Morsi sit-ins in Cairo. Another 10 people have reported being tortured and accused of being spies by the protesters there. All officials spoke anonymously because they were not authorized to speak to the media.
Separately, a man who appeared to be a pro-Morsi supporter was killed when his store was burnt by a mob in the city of Port Said on Sunday. It was the third death in Port Said that day. Earlier, two people died when fighting broke out at a funeral for one of the 83 killed in clashes with police in Cairo.
Associated Press writer Maggie Michael contributed to this report.
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