A ministry source put the number of people injured at 120.
One eyewitness said the two trains mounted into the air "forming a pyramid" after they slammed into each other at a suburban station on the edge of the Mediterranean port city.
The stationary train had just arrived from Port Said, a Mediterranean city on the northern tip of the Suez Canal, when it was hit.
The initial reports said the human causalities reached 25 person، and dozens others injured.
In 2016, a train derailed in south of Cairo, killing five people, and injuring 27 people in the al-Ayat area.
After nightfall, cranes aided by floodlights began to remove the wreckage off the tracks to allow rail traffic to resume.
Egypt's Health Ministry has raised to 36 the death toll from a train collision just east of the coastal city of Alexandria. Rescue teams, meanwhile, continued to look for more bodies and injured passengers inside the carriages.
Hospitals in Alexandria announced state of emergency to receive more injured.
Egypt's railway system has a poor safety record, mostly blamed on decades of badly maintained equipment and poor management.
Train accidents are common in Egypt.
It was the deadliest train accident in the North African country since a train ploughed into a bus carrying schoolchildren in November 2012, killing 47 people.
One resident, Hoda, was standing on her rooftop when she saw the trains collide. It is not yet known what caused the two trains to collide.