Military commander-in-chief Abdel Fattah El-Sisi has called for nationwide rallies on Friday to mandate the armed forces and police to crackdown on "violence and terrorism," following a series of violent clashes across the country.

"Nevertheless this does not mean I am advocating for violence or terrorism," El-Sisi said in a speech at a military graduation ceremony in Alexandria on Wednesday.

"I call on all political powers to join the efforts for national reconciliations," the commander-in-chief said.

The first round of national conciliation, which will start on Wednesday under the auspices of the interim president Adly Mansour, will not be attended by the Muslim Brotherhood, the group from which the ousted president Mohamed Morsi hails, or its political arm the Freedom and Justice Party.

A number of Islamist groups and parties that form the National Alliance to Support Legitimacy also decided to boycott the meeting.

The meeting will be attended by several political forces including the National Salvation Front, the Wafd Party and the Egyptian Social Democratic Party.

Thousands of Morsi supporters are holding an ongoing sit-in at Rabaa Al-Adawiya Square in Cairo and Nahda Square in Giza demanding his reinstatement.

More than 100 people have been killed in violent clashes since Morsi’s removal, pitting his supporters against his opponents and security forces.

Marches from both sides have been repeatedly attacked by armed men. The use of live rounds has been common in recent weeks amid an increase in violent protests across the country.

"El-Sisi and the intelligence are instructing the interior ministry to commit those crimes against peaceful protesters who are being punished for merely saying no to the military coup," Brotherhood leading member Mohamed El-Beltagy said.

El-Sisi’s call comes a few hours after an explosive device went off at a police station near the security directorate in the Nile Delta city of Mansoura, the capital of Daqahliya governorate, killing at least one conscript and injuring 19 late on Tuesday.

Clashes in the restive Sinai Peninsula between the army and Islamist militants have also left dozens dead since deposed president Morsi was removed from his post by the military on 3 July amid massive protests.

Morsi supporters accused El-Sisi, who was assigned his post by former president Morsi, of betraying and conspiring against him, calling the army's move a "military coup."

"I did not deceive the former president," El-Sisi said, denying accusations of his betrayal.

"We advised the former president several times since the November Constitutional declaration," he said, adding that his advice was ignored by Morsi.

"The former president was advised, directly and indirectly, either to step down or hold a referendum to see if the people want him or not," El-Sisi stated. He added that he sent the former prime minister Hisham Qandil, former head of Shura council Ahmed Fahmy, and former Islamist presidential candidate Selim El-Awa to Morsi with the suggestions.

"I made it clear that the army is under his commandership only as the president according to the legitimacy he was granted from the people," El-Sisi added.

"We are ready to have the whole world supervise the elections, including the UN and the EU," he stressed, referring to presidential elections expected to be held within six months. "We are not retreating from the roadmap we adopted." 

The commander-in-chief denied that there are any defects or splits in the Egyptian army.

Morsi has been held incommunicado in an unidentified location since his ouster. The army said that such a measure was taken to protect him.