Egyptian police broke up a Muslim Brotherhood sit-in near the Giza zoo and attempted to clear the other at Rabaa El-Adawiya square shortly after dawn on Wednesday, making good on pledge to disperse thousands of Islamists in both venues.
The ambulance authority said 13 were killed and at least 94 wounded but the Brotherhood put the death toll at 121, citing a makeshift hospital at the Rabaa sit-in. An AFP correspondent said he had counted 43 dead bodies.
Egypt's state television said two police personnel, an officer and a conscript, were killed and six wounded during the attempt to clear out the two sit-ins.
Two hundred Brotherhood protesters at both camps were arrested for possessing firearms, bladed weapons and gas canisters, state news agency MENA reported.
The railway authority said it had stopped all train services in and out of Cairo "for security reasons and to prevent people from mobilising".
"In accordance with government instructions to take necessary measures towards the sit-ins at Rabaa Al-Adawiya and Nahda, and for the safety of the country, security forces started taking measures to disperse the sit-ins early Wednesday," the interior ministry said in a statement.
"There are paths available for those who are present in the sit-in from which they can safely exit."
Live television footage showed riot police firing tear gas at protesters at one of the entrances of Rabaa El-Adawiya mosque in northern Cairo, where tens of thousands have been camping for six weeks to demand the reinstatement of ousted President Mohamed Morsi.
All entrances to Rabaa were later blocked by security forces. Brotherhood spokesman Gehad El-Haddad accused police snipers of firing at Rabaa protesters from the rooftop of surrounding buildings.
Al-Nahar and ONTV satellite channels said their cameras were confiscated by police forces while covering the attempt to disperse the Rabaa sit-in.
At the Nahda camp, centred round a traffic circle and extending down a palm tree-lined boulevard next to the Cairo zoo in Giza, greater Cairo, police used loudspeakers to urge protesters to leave as sounds of gunfire rang out.
"Armed men in both camps fired at police forces once they started dispersing the sit-ins ... police were able to control Nahda and are still combing the surrounding area," the interior ministry said in another statement on its official Facebook page.
"The police forces only used tear gas despite being attacked by live ammunition [from protesters]."
Police officers were videoed brandishing bullets they said had been captured from the Rabaa sit-in.
Around 300 have been killed in clashes pitting the supporters of Morsi against his opponents and security forces since the army ousted Egypt's first freely elected president on 3 July.