Khaled el-Khateeb, head of the ministry's emergency and intensive care department, says another eight died in clashes in the Mediterranean city of Alexandria.
In a statement today, he said 792 people were wounded in both incidents, which spanned for the last two days.
The Cairo violence took place when pro-Morsi protesters sought to expand their sit-in camp by moving onto a nearby main boulevard, only to be confronted by police and armed civilians.