A spokesman for Egypt's health ministry, Khaled Megahed told al-Ahram the death toll was 36 with more than 100 people injured.
One of them had been heading from Cairo to the northern city of Alexandria and the other from the canal city of Port Said, east of the capital, to Alexandria.
Alexandria, Egypt's second-largest city, sits on the Mediterranean coast in the north.
According to local authorities, a mistake by the operator of a semaphore caused the accident.
People gather at the site of a train collision in the area of Khorshid, in Egypt's Mediterranean city of Alexandria. Residents from nearby homes rushed to the scene to look for survivors inside crushed train carriages or offer first aid to the injured.
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Bizarrely, this is the second time in less than a year that a vehicle has fallen off the edge of the same parking garage. Dramatic CCTV footage has been released of a woman's auto plunging seven stories off the side of a parking garage.
"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.
Egyptians have long complained that the government has failed to deal with chronic transport problems, with roads as poorly maintained as railway lines.
Train accidents are common in Egypt. Figures recently released by the state's statistics agency show that 1,249 train accidents took place past year, the highest number since 2009 when the number reached 1,577.
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.
Efforts were still exerted to extradite more bodies and injured from wreckage of the two trains.