Abdel-Fattah el-Sissi's remarks Thursday came a day after a passenger train collided with a cargo train north of Cairo, killing at least 12 people, including a child, and injuring 39.
The crash between a freight train and a passenger train occurred at Kom Hamada in Behaira province. Civilians and medics were seen removing injured passengers and carrying them to ambulances.
The cause of the accident was not immediately known.
Nineteen people have died and forty more injured, according to Health Ministry. Figures recently released by the state's statistics agency show that 1 249 train accidents took place previous year, the highest since 2009 when the number reached 1 577.
The probe, however, did not prevent further accidents.
Egyptians have long complained that successive governments have failed to enforce basic safety measures for the railways.
Egypt witnessed a number of deadly train accidents over the past few years in which hundreds were killed and wounded. The train sped for miles, with flames engulfing one carriage after another, killing more than 370 people.
The death toll has reportedly risen to 15 people with 40 injured.