But investigators concluded that no donkey-meat had been marketed for human consumption, police sources said on Sunday.
The butchers had apparently been selling the animals to Cairo zoo to feed its tigers and other big cats.
But interior ministry police arrested four employees of the zoo, including two butchers, who were charged with violating environmental protection laws by not disposing of the bodies in a designated area.
The remains of nine donkeys were found on Friday in a dump in al-Bahr al-Azam street in Giza, a city next to Cairo, not far from the zoo.
Fear had reportedly gripped the neighbourhood after the discovery, apparently owing to the Muslim belief that consumption of donkey meat is religiously doubtful.
But residents were scared butchers could be seizing on the increase in meat consumption during the Muslim fasting month of Ramadan to sell donkey meat and boost their profits.
Meat prices have risen in Egypt along with other commodities after the local pound lost nearly 25% of its value against the dollar following its flotation in late January.