This is the deadliest train accident in the country since a November 2013 collision between a train and a bus killed 27 people south of Cairo.
After nightfall, cranes aided by floodlights began to remove the wreckage off the tracks to allow rail traffic to resume.
The Health ministry is yet to announce the final toll.
The dead and injured were initially placed on blankets by the sides of the tracks amid farmland on the outskirts of Alexandria
The number of people who died in a two-train collision in the suburbs of the Egyptian city of Alexandria increased to 41, while 179 people were injured, Egypt's Al-Ahram newspaper reported Friday, citing the Health Ministry.
"The rescue team is now searching for survivals while ambulances are transferring the injured to nearby hospitals", said Magdy Hegazi, undersecretary at the Health ministry.
Nearly a year later, a collision between a train and a bus killed 27 people south of Cairo.
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The stationary train had just arrived from Port Said, a Mediterranean city on the northern tip of the Suez Canal, when it was hit.
Train accidents in Egypt are rare but not unheard of.
Some people were still stuck inside the trains, a medical official told state TV. Figures recently released by the state's statistics agency show that 1,249 train accidents took place previous year, the highest number since 2009 when the number reached 1,577.
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At least 360 people were killed in 2002 in Egypt's worst train disaster when a major fire engulfed seven carriages of an overcrowded passenger train. It is not yet known what caused the two trains to collide.
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Low temperatures have been below normal, high temperatures have been slightly below normal, and the air has been unseasonably dry. A weak cold front is expected to bring cooler temperatures and a chance of showers and thunderstorms through the weekend.