Another 40 people were hurt in the collision between a freight train and a passenger train in Beheira province, it said in a statement.
Egyptians have long complained that successive governments have failed to enforce basic safety measures for the railways. A string of crashes have further inflamed public anger over the antiquated transport network.
Footage aired by state television showed at least two carriages had derailed in a rural stretch of land. Civilians and medics were seen removing injured passengers and carrying them to ambulances.
Health ministry official Alaa Othman told state television “all the wounded and dead have been removed from the scene of the accident”.
The cause of Wednesday’s crash was not immediately clear. Prime Minister Sherif Ismail ordered Transport Minister Hesham Arafat to visit the scene and take action as details of the causes of the accident emerge, a cabinet statement said.
The crash comes months after 41 people died in a train collision near the coastal city of Alexandria last August.
That was the deadliest train accident in Egypt since a November 2013 collision between a train and a bus killed 27 people south of Cairo.
In 2002, 373 people died when a fire ripped through a crowded train, also south of the capital.
Figures recently released by the state’s statistics agency show that 1,249 train accidents took place last year, the highest since 2009 when the number reached 1,577.