In 2002, 373 people died when a fire ripped through a crowded train south of the capital.
Friday's crash was the latest in a series of deadly accidents that have claimed hundreds of lives over the years.
By nightfall, cranes aided by floodlights began to remove the wreckage off the tracks to allow rail traffic to resume.
"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.
A health ministry spokesman said 75 ambulances had been deployed at the crash scene.
Another train derailment in Badr Rashin in Giza killed at least 19 people in 2013.
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.
According to local authorities, a mistake by the operator of a semaphore caused the accident. "When we came out, we found four train cars crushed and a lot of people on the ground".
Assistant health minister Sharif Wadi told state television that most of the injured had been taken to hospital.
As many as 28 people were killed and 80 injured after two trains collided in the Egyptian city of Alexandria.
Two senior medical officials in Alexandria, Mohammed Abu Homs and Magdy Hegazy, gave the casualty tolls for the tragedy on Friday, cautioning that the death toll was likely to rise further.