The anti-Mursi protesters were staging a sit-in outside the palace when they were attacked.
Earlier U.S. Secretary of State Hillary Clinton had said that the situation in Egypt is critical and said that a dialogue is ‘urgently needed’ keeping in scenes in the streets of Cairo.
Former presidential candidate Amr Moussa, who is also chairman of the Egyptian National Congress, warned that the clashes will further heat up the situation.
The Constitution Party also warned of "dire consequences" for what it described assaults on peaceful protesters in Tahrir Square and outside the palace.
"We are warning of dire consequences for mounting calls by figures affiliated with the Muslim Brotherhood and the Islamist current," the party said in a statement, which claimed that the president's supporters had called for massive protests "and even jihad, according to Al-Misry-al-Youm.
The clashes came after Mursi, who yesterday left the Palace through back gate, today returned to the complex.
Meanwhile, Prosecutor General Talaat Ibrahim Abdallah yesterday ordered a probe against three former presidential candidates accusing them of espionage and conspiring a "Zionist plot" against the Islamist government.
Abdallah referred to the State Security Prosecution a complaint accusing Mohamed ElBaradei, Hamdein Sabahy and Moussa of spying and inciting the overthrow of the President.
Founder of the Constitution Party ElBaradei, Moussa and founder of the Popular Current Party Sabahy have declared their support to the ongoing anti-Mursi protests after the latter assumed absolute power through a decree last month, sparking the current crisis.
Hamed Sadeq, a lawyer who filed the complaint, also accused Wafd Party president Al-Sayed al-Badawy and Judges Club head Ahmed al-Zend of espionage and sedition.
Sadeq claimed that Moussa met with former Israeli foreign minister Tzipi Livni and agreed with her to fabricate internal crises, and that all of the politicians named in his complaint then met at the Wafd Pary headquarters here to implement the "Zionist plot."
He requested that the accused be banned from travel and that the Wafd Party headquarters be confiscated for probe.
Filing criminal charges against opposition figures was a common practice during ousted president Hosni Mubarak's era.
Ghad al-Thawra Party leader Ayman Nour was sentenced to five years in prison in December 2005 for allegedly forging signatures to enable him to register the Ghad Party.
The party had been approved in 2004. Nour was released from prison in February 2009.
Nour finished second after Mubarak in the presidential election in September 2005. Some observers argued that the case was punishment for his unexpected bid for presidency.
Cairo: Clashes broke out Wednesday night between Muslim Brotherhood members and opposition supporters in front of the high-security Egyptian presidential palace here where the two groups assembled for rival demonstrations after Islamist President Mohamed Mursi returned to the complex.
First Published: Wednesday, December 05, 2012, 21:10