The drivers of the two trains that collided on Friday have been held for questioning and four railway officials suspended pending the results of a probe into its causes, Transportation Minister Hisham Arafat told an Egyptian broadcaster.
Under floodlights, rescue teams had combed wrecked carriages all night for casualties.
Transport ministry officials, quoted on state television, have said the crash in farmland on the outskirts of Alexandria was probably caused by a malfunction in one train that brought it to a halt.
The other train then crashed into it.
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.
“We have a big problem we had already announced, which is old traffic signals. We are completely overhauling them. This section here is being developed,” he said.
An injured passenger who was on the stationary train said its departure had been delayed and that it kept stopping en route.
“It stopped every now and then between stations or before stations for five minutes, I don’t know why,” the man told Dream television station from his hospital bed.
“Everyone was scattered (by the collision), bodies were flung around,” he said.
The toll from Friday’s accident when the two trains collided near Alexandria rose to 41 dead, the health ministry said on Saturday.
The accident also wounded 132 people, with 79 being discharged after treatment while 53 remained in hospital on Saturday, Health Minister Ahmed Emad el-Din Rady said.
A stream of ambulances had ferried the injured, stretched out on the ground in a field alongside the railway tracks, to Alexandria hospitals.
Workers used cranes to lift four knotted sheet-metal carriages blocking the normally busy Cairo-Alexandria line.
One train had been heading to Alexandria from Cairo and the other from Port Said, east along the coast.
President Abdel Fattah al-Sisi has sent his condolences to the victims’ families and ordered a probe to “hold accountable” those responsible for the disaster.