The accident occurred before dawn when the 12-carriage train carrying 1,328 Egyptian army conscripts heading toward Cairo, crashed into a cargo train, Hussein Zakareya, head of Egypt's Railway Authority, told Ahram Online.
A health ministry official said the death toll is expected to rise as many of the injured are in critical condition.
Ambulances transported the injured to a nearby hospital as police searched the rubble.
"We have to admit that the railway system is decaying. We will carry out investigations to know whether the accident happened because of defects in the train or rails or because of other reasons," Transport Minister Hatem Abdel-Latif told Ahram Online.
The incident occurred just months after some 50 schoolchildren were killed when their bus was hit by a train in November, the website said. The same month, in another train accident, three Egyptians were killed and more than 30 injured.