The bus carrying students between the age of four and eight was hit by the speeding train near al-Mandara village in Manfalut district of Assiut province. The ill-fated bus was headed towards a religious institute in Aswan where the children studied.
According to reports, the bus driver tried to cross the tracks as the barriers were not in place. The provincial governor Yahya Keshk told state television that the level crossing worker was asleep at that time.
Following the impact, the bus was pushed around one kilometre by the speeding train. Most of the bodies recovered from the accident site were found to be badly mutilated.
Eyewitnesses said that relatives of the victims were desperately trying to "collect the remaining body parts" and had blocked the nearby road to register their protest. The authorities assured the distraught protesters that they will be provided all the possible help.
Transport Minister Rashad al-Metini and Egyptian Railway Authority chief Mostafa Qenawi have already put in their papers, owning moral responsibility for the accident.
President Mohamed Morsi accepted the resignations and ordered all the officials concerned "to offer all assistance to the families of the victims". Prime Minister Hisham Kandil ordered an investigation into the accident.
Egypt's worst railway disaster was in Feb 2002 when seven bogies of a passenger train caught fire, killing as many as 360 of the passengers.