It is thought to be the deadliest rail accident since November 2013 when a train hit a bus south of Cairo, killing 27 people.
"We ran to the scene and we found people jumping from the train and lots of dead", said Abdel-Bari Abdel-Hamid.
Magdy Hegazy, a top health official in Alexandria, says the crash also injured 122 people.
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Friday's accident took place less than a month before Eid al-Adha, a major Muslim festival during which Egyptians usually depend on trains to travel to their hometowns for family reunions. Inhabitants from close-by homes raced to the scene to search for survivors inside smashed prepare carriages or offer emergency treatment to the harmed. It is not yet known what caused the two trains to collide.
Egypt's transport minister has ordered an investigation into the crash, Nile TV reported.
An Egyptian health official has further raised the death toll from a train collision just east of the coastal city of Alexandria, saying that 43 people were killed.
Footage shows dozens of people crowding around the damaged train cars, with bodies strewn on the ground.
But that pales in comparison to the 370 or more who died when a massive fire swept through an overcrowded train going from Cairo to Luxor in 2002.