Mohammed Fathallah, the ministry spokesman, said earlier that the blood-soaked bodies lined up in the El Imam mosque in Nasr City were not included in the official death toll. It was not immediately clear if the new figures included the ones at the mosque.
Inside the mosque-turned-morgue, the names of the dead were scribbled on white sheets covering the bodies, many of them charred, and a list with 265 names was plastered on the wall. Heat made the stench from the corpses almost unbearable as the ice brought in to chill the bodies melted and household fans offered little relief.
Over the mosque speakers, announcements urged people to leave because their body heat was making the humid conditions worse inside the mosque, where posters of Morsi were piled up in a corner.
Many people complained that authorities were preventing them from obtaining permits to bury their dead, although the Muslim Brotherhood announced that several funerals had been held Thursday for victims who had been identified. Fathallah denied that permits were being withheld.
Omar Houzien, a volunteer helping families search for their loved ones, said the bodies were carried to the mosque from a medical center at the protest camp in the final hours of Wednesday's police sweep because of fears that they would be burned.
Elsewhere, a mass funeral was held in Cairo for some of the 43 security troops who authorities said were killed in Wednesday's clashes. Interior Minister Mohammed Ibrahim, who is in charge of the police, led the mourners. A police band played solemn music as red fire engines bore the coffins draped in white, red and black Egyptian flags in a funeral procession.
Morsi's Muslim Brotherhood put the casualty toll at a staggering 2,600 killed and around 10,000 injured, but the figures appeared high in light of footage by regional and local TV networks, as well as The Associated Press.