Local media reports suggest that one of the trains was travelling from Port Said and the other from Cairo, before they crashed head-on, reports The Independent.
Footage showed dozens of people crowding around the damaged train cars, with bodies on the ground.
After nightfall, cranes aided by floodlights began to remove the wreckage off the tracks to allow rail traffic to resume.
The crash also injured 123 people, the ministry said in a statement.
At least 36 people were killed and over 120 others injured in Egypt after two trains collided near the coastal city of Alexandria, officials said.
Train accidents in Egypt are rare but not unheard of.
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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, according to the statement.
People gather at the site of a train collision in the area of Khorshid, in Egypt's Mediterranean city of Alexandria.
Assistant health minister Sharif Wadi told state television that most of the injured had been taken to hospital.
That accident came months after a train carrying military conscripts derailed, killing 17 people, and nearly a year after 47 schoolchildren were killed when a train crashed into their bus.