The Muslim Brotherhood has warned of a possible massacre if police forcibly disperse two pro-Morsi sit-ins in the Egyptian capital.

Brotherhood spokesperson Ahmed Aref was speaking after the country's interim leaders ordered police to end ongoing protests at Rabaa Al-Adawiya in Cairo's Nasr City and Nahda Square in Giza.

"This upcoming massacre is clear now. It is targeting millions of protesters against the military coup," Aref told Al-Ahram Arabic news website on Thursday.

"It is not about [deposed president Mohamed] Morsi or the Muslim Brotherhood; those millions in the squares are rejecting the coup against [democratic] legitimacy," Aref said.

He insisted pro-Morsi protesters had been peaceful and had never resorted to violence.

"There are no weapons at the sits-ins," he said, "it is only a lie to justify their dispersal by force which will result in hundreds of victims."

Brotherhood spokesperson Gehad El-Haddad also condemned the order to disperse the protests.

"They tried to disperse the sit-ins twice before and failed, killing at the same time 200 protesters. Would they want to try this again?" El-Haddad told AFP on Wednesday.

"We do not recognise this government or its powers or the laws it represents," El-Haddad said in separate comments to Reuters.

Essam El-Arian, vice chairman of the Brotherhood's Freedom and Justice Party, said via Facebook on Thursday, "Our cause is just and our sit-in is peaceful, our peacefulness is strong than bullets. Our will is strong, the psychological warfare and lies will not affect our morale. The people will prevail against the coup."

The Brotherhood's Mohamed Ali Beshr said on Wednesday that dozens of diplomats, journalists and human rights activists had visited the sit-ins and found them to be peaceful. People can visit the protests at any time, he insisted.

There are accusations that protesters at both sits-ins have stockpiled weapons.