Rescuers were battling to save casualties on Wednesday morning after the major fire, but the death toll from the accident is "likely to rise".
"There are records that show which driver is in which railcar", he said. In general, he said, the accident suggested "negligence from the driver and supervisors".
Dozens of ambulances and fire engines rushed to the scene.
Egyptian Transport Minister Hesham Arafat has tendered his resignation because of the incident, according to Egypt's state news wire, and the prosecutor general has ordered an investigation into the fire.
The Ramsis district is among the busiest and most crowded areas of the Egyptian capital.
Flames have spread to nearby buildings, causing them to collapse, after the train slammed into the platform on Wednesday. A man is seen running back and forth, his shirt on fire, until another man rushes to pour water on him.
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Prime Minister Mustafa Madbouli vowed harsh punishment for those behind the accident.
Egypt's railway system is badly in need of crucial upgrades and a fresh injection of funds, but the economy is doing badly.
The official statistics agency says there were 1,793 train accidents in 2017, up from 1,249 in 2016.
The National Railway Authority said a train collided with a concrete buffer stop at the central Ramses Station.
In March past year, the president said the government lacked about 250bn Egyptian pounds (£10.7bn; $14.1bn) to overhaul the rundown rail system.
In August 2017, 43 people died when two passenger trains collided outside Alexandria.