A security operation to clear protesters camped out on the streets of Cairo since President Mohamed Morsi was deposed by the military last month has left at least 40 people died.

The Egyptian Interior Ministry says 200 people have been arrested, including 50 in the Rabaa al-Adawiya sit-in in Nasr City and 150 at the Nahda Square sit-in in Giza.

Live footage from Cairo on Wednesday morning showed smoke engulfing Nahda Square - which was later completely cleared - and there were reports of tear gas and birdshot being used on supporters of the Morsi.

By mid-morning, state television reported that security forces had finished breaking up the sit-in there.

Bulldozers were said to have been used to uproot the camps.

The Interior Ministry said security forces had "total control" over Nahda Square, and that "police forces had managed to remove most of the tents" in the area. Security forces had blocked all access to the protest camp.

Conflicting toll figures

Sources on the ground told Al Jazeera of at least 40 fatalities, while the Muslim Brotherhood said at least 300 people had been killed, with more than 5,000 others injured.

Al Jazeera could not independently verify the Brotherhood's figure.

The Health Ministry said at least seven people had been killed, including three members of the security forces, and 78 injured.

State television also said a number of people were arrested in Nasr City for having weapons and gas cylinders.

The Interior Ministry warned in a statement that the forces would deal firmly with protesters acting "irresponsibly" and said it would guarantee safe passage to those who want to leave the sites.

Al Jazeera's Rawya Rageh, reporting from Cairo, said: "This battle is much bigger than what you're seeing and the casualties. This is a fight for the future of the country, and something that will determine the course of the Egyptian revolution that has been going on for two years now.

"No one expected this to be an easy operation. It became very clear that both sides were engaged in a battle of wills and a dangerous game of brinkmanship."

Khaled Daoud, spokesperson for the National Salvation Front, one of the main opposition blocs against Morsi, told Al Jazeera: "These sit-ins, which are not peaceful at all, have been around for nearly 48 days, blocking main roads … All of those sit-ins were the HQs from which demonstrations go out to nearby military installations, security installations, they clash with people ... several incidents in which weapons have been seen with supporters of the Mulsim Brotherhood.

"We've been living in a standstill for the past 48 days, cannot move around the city, storming government ministries … not peacefully oriented or intended."

In response to the security operation, the Muslim Brotherhood urged Egyptians to take to the streets to "stop a massacre".

"This is not an attempt to disperse, but a bloody attempt to crush all voices of opposition to the military coup," Brotherhood spokesman Gehad al-Haddad said on Twitter.

The organisers of the protest in Rabaa al-Adawiya, where several Brotherhood leaders were present, "is calling on Egyptians to take to the streets to stop the massacre", Haddad said.

Traffic blocked

Al Jazeera's D. Parvaz said she was prevented from accessing the Rabaa al-Adawiya site and that "there is absolutely no access to the sit-in except for police and medical services".

"Pro-Morsi supporters are making calls to their supporters, including those in other governorates, to tell them to join the protest," she said.

She said all traffic in the area had been blocked.

Laila, a member of Egypt's Anti-Coup Alliance, a pro-Morsi group, said: "Many people are being killed right now . What we can expect is only worse.

"What's happening now is a crime against humanity."

Wednesday's crackdown follows weeks of warnings from the interim Egyptian leadership that force would possibly used to clear the protesters.

At least one person was killed on Tuesday, and many others injured in clashes between supporters and opponents of Morsi, who was removed from power by the militarr on July 3.