Egyptian security forces have entered a mosque in Cairo to end a stand-off with around 700 Muslim Brotherhood supporters who had spent the night barricaded inside.

Special forces had surrounded al-Fateh mosque in Ramses Square after Morsi supporters spent the night holed up inside following a day of violence in which at least 95 protesters died.

Witnesses said hundreds of those inside managed to escape the mosque moments before special forces entered, and were seen streaming out from a side door after the forces briefly withdrew.

The mosque had become a makeshift morgue and field hospital for the Brotherhood during a day of clashes that spilled out from the square.

The Brotherhood had called for a "day of rage" after at least 630 protesters were killed when the army cleared Muslim Brotherhood camps in Cairo on Wednesday. The movement has called for another week of daily rallies.

Brotherhood supporters have been protesting since last month, when the army forced Morsi to step aside.

Live TV footage showed security services in riot gear entering the mosque on Saturday.

Security officials said "armed elements" had opened fire from inside the mosque, Egypt's stete-run Mena news agency reported.

Brotherhood supporters inside the mosque had called on the security forces to move away from the area before they evacuated the buidling.

Egypt's interior ministry said in a statement that 1,004 "Muslim Brotherhood elements" had been arrested on Friday. The ministry said 558 of the arrests took place in Cairo.

Egypt's interim leaders have imposed a state of emergency with dusk-to-dawn curfews in the capital and other areas.

The interior ministry says police have been authorised to use live ammunition "within a legal framework".

Elsewhere on Friday, at least five people were killed in Alexandria, six in Suez, eight in Damietta and five in Fayoum, according to medical sources.