El-Khateeb said 202 of the 525 were killed in the Nasr City protest camp, but it was not immediately clear whether the bodies at the mosque were included in that figure. Another Health Ministry spokesman, Mohammed Fathallah, said he had no knowledge of the bodies at the el-Iman mosque.
Victims' names were scribbled on white sheets covering their bodies, some of which were charred. Posters of Morsi were scattered on the floor.
"They accuse us of setting fire to ourselves. Then, they accuse us of torturing people and dumping their bodies. Now, they kill us and then blame us," screamed a woman in a head-to-toe black niqab.
Omar Houzien, a volunteer helping families search for their loved ones, said the bodies were brought in from the Medical Center at the sit-in camp site in the final hours of Wednesday's police sweep because of fears that they would be burned.
A list plastered on the wall listed 265 names of those said to have been killed in Wednesday's violence at the sit-in. Funerals for identified victims were expected to take place later on Thursday.
Meanwhile, a mass police funeral — with caskets draped in the white, red and black Egyptian flag — was held in Cairo for some of the 43 security troops killed in Wednesday's clashes.
Interior Minister Mohammed Ibrahim, who is in charge of the police, led the mourners. A police band played funerary music as a somber funeral procession moved with the coffins placed atop red fire engines.
Wednesday's violence started with riot police raiding and clearing out the two camps, sparking clashes there and elsewhere in the Egyptian capital and other cities.
Cairo, a city of some 18 million people, was uncharacteristically quiet Thursday, with only a fraction of its usually hectic traffic and many stores and government offices shuttered. Many people hunkered down at home for fear of more violence. Banks and the stock market were closed.