Twelve people died and 39 were injured in the crash between a freight train and a passenger train at Kom Hamada in Behaira province, health ministry spokesperson Khaled Mehaged told state television, updating an earlier casualty toll.
Footage aired by the 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 that all casualties had been removed from the scene of the accident.
The provincial governor Nadia Abdou said that the crash happened at around 1045 GMT and that its cause was "unknown".
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The state prosecutor announced that a team of investigators had been dispatched to probe the accident.
While the cause of the crash remains unclear, it comes months after 41 people died in a train collision near the coastal city of Alexandria last August.
The train drivers who survived that accident were detained for questioning.
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.
It came a year after a train smashed into a bus carrying school children, killing 47 people.
That accident jolted the government which ordered an investigation and sacked the transport minister and the head of the railway authority.
It was blamed on a train signal operator who had fallen asleep on the job.
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The probe, however, did not prevent further accidents. Months later a train carrying military conscripts derailed, killing 17 people.
Egyptians have long complained that the government has failed to deal with chronic transport problems, with roads as poorly maintained as railway lines.
The deadliest accident on Egypt's railways dates back to 2002 when 373 people died as a fire ripped through a crowded train south of the capital.
There have been many other fatal crashes on the busy rail network.
In July 2008, at least 44 people died near Marsa Matruh in northwest Egypt when a runaway truck hurtled into a bus and several other vehicles waiting at a level crossing, shunting them into the path of a train.
In August 2006, at least 58 Egyptians were killed and 144 injured in a collision between two trains travelling on the same track.
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