Some 25 people are dead and 65 injured, it was reported.
Arafat had told reporters at the scene of the accident that it was not yet clear why the train had stopped, but suggested old traffic signals were to blame. Residents from nearby homes rushed to the scene to look for survivors inside crushed train carriages or offer first aid to the injured.
The country's chief prosecutor, Nabil Sadeq, ordered an urgent probe into the accident. Train accidents are not common in the country but there have been a few in the last 20 years. "When we got out of the vehicle, we saw four crushed cars and a lot of people lying on the ground".
At least twenty killed, scores injured after Egypt trains collide head-on
In addition, according to some, a work station filed the wrong signal to the first composition, for which the train stopped, and he later entered other composition.
Egypt has witnessed a number of deadly train accidents causing hundreds dead and injured.
Passenger Moumen Youssef said: "The train I was riding was going very quickly. When we came out, we found four train cars crushed and a lot of people on the ground", he said.
However, the ministry also said that the number of casualty may rise due to the seriousness of many injuries.
One resident, Hoda, was standing on her rooftop when she saw the trains plow into each other.