Egypt's public prosecutor on Saturday referred 48 people to trial for their involvement in deadly Muslim-Christian clashes last month.

The 48 accused were referred to Cairo's supreme state security court for "premeditated murder, endangering public security, inciting sectarian tension, burning a church and possessing weapons with the intent to carry out acts of terrorism," the prosecutor's office said.

Fierce clashes broke out on 7 May between Christians and Muslims in northwest Cairo's working-class district of Imbaba where 12 people were killed, scores injured and a church set ablaze, according to court figures.

The National Council for Human Rights, however, put the death toll at 15.

Of the 48 accused, 22 are in preventative detention and the search continues for the remaining 26, the prosecutor said.

Egypt has been gripped by chronic insecurity and sectarian strife. 

Coptic Christians, who account for up to 10 per cent of Egypt's 80-million people, complain of discrimination and have been the targets of sectarian attacks.