Egypt’s security forces have stormed two protest camps occupied by supporters of deposed President Mohammed Morsi in Cairo, killing at least 30 of them.

Armoured bulldozers moved deep into the main camp outside the eastern Rabaa al-Adawiya mosque and another protest camp at Nahda Square, pulling down all the tents used as shelter by the protesters.

There was no official confirmation of the death toll but witnesses said they saw at least 40 bodies, while the Muslim Brotherhood claim that hundreds died.

The health ministry said 13 people were killed near Rabaa during the crackdown, including five police and eight civilians.

The operation, which suggested that the powerful military had lost patience with persistent protests that were crippling parts of the capital and slowing the political process, began just after dawn with helicopters hovering over the camps.

The protesters, among them women and children, fled Rabaa for safety as the sound of gunfire and clouds of black smoke rose into the air.

The government issued a statement saying security forces had showed the “utmost degree of self-restraint”, reflected in low casualties compared to the number of people “and the volume of weapons and violence directed against the security forces”.

At least 20 were shot in the legs as television pictures showed security forces shooting from nearby rooftops.

“Tear gas (canisters) were falling from the sky like rain. There are no ambulances inside. They closed every entrance. There are women and children in there. God help them. This is a siege, a military attack on a civilian protest camp,” said protester Khaled Ahmed, 20, a university student wearing a hard hat with tears streaming down his face.

The 17-year-old daughter of leading Muslim Brotherhood figure Mohamed el-Beltagy was among the dead. Asmaa al-Beltagy was shot in the back and chest, her brother said.

The operation came after international efforts failed to mediate an end to the political standoff between Mursi’s supporters and the army-backed government which took power after his ouster on July 3.

Meanwhile, there were also reports of violence in other parts of Egypt.

State news agency Mena says three churches were attacked in central Egypt, one in the city ofSohag with a large number of Coptic Christian residents.

Security sources quoted by Reuters news agency reported clashes between security forces andMorsi supporters in Assiut and Minya cities.

Morsi supporters are reported to have blocked roads in the northern city of Alexandria.

Hundreds are said to have gathered outside the governor’s office in Aswan in the south and the interior ministry said a mopping-up operation in the streets surrounding Nahda Square was under way.

Egypt has been engulfed by political and economic turmoil since a 2011 uprising that ended 30 years of autocratic rule by ousted President Hosni Mubarak.