However, the ministry also said that the number of casualty may rise due to the seriousness of many injuries.
Earlier in the day, an train from Cairo to Alexandria crashed into the rear of another train on its way from Port Said to Alexandria, leaving dozens killed and injured.
The accident took place in Kourshid area, east of the coastal city of Alexandria.
Right after the collision, Egypt's general prosecutor ordered an urgent investigation into the accident.
Egyptian President Abdel-Fattah al-Sisi has also ordered state bodies to hold those responsible accountable.
Egypt has witnessed a number of deadly train accidents causing hundreds dead and injured.
In 2013, at least 19 were killed in a train derailment in Giza governorate, while a collision in 2012 between a train and a school bus in Upper Egypt killed 51 people, mostly children.
More than 36 people were killed and 120 injured in a train collision in the Egyptian coastal city of Alexandria yesterday.
One train had been travelling from the capital Cairo, the other from Port Said in the north, when they crashed head-on at speed during Friday evening rush hour.
Transport ministry officials said the accident was probably caused by a malfunction in one of the trains that brought it to a halt on the rails. The other train is then thought to have crashed into it.
In pictures circulated on social media, nearly a dozen wounded and dead could be seen lying next to the crash site covered in blankets.
Dr Mohamed Abu Homs, the head of the ambulance services in Alexandria's western sector, said he fears the death toll and the number of injured could rise further.
Egypt's transport minister ordered an investigation into the crash, pledging to "hold accountable" whoever was responsible.
An Egypt Railways official told the Telegraph that both of the trains were coach class only.
At this time of the year, trains heading to Alexandria are usually crowded with Egyptians escaping the hot weather in the mainland to the cooler beaches in the north.
Egypt's railway system has a poor safety record, mostly blamed on decades of badly maintained equipment and poor management.
Egyptians have long complained that the government has failed to deal with chronic transport problems, which has done little to improve its roads and railway lines in recent years.
It is the deadliest train accident in the North African country since a November 2013 collision between a train and a bus killed 27 people south of Cairo. Many of those were relatives who had been returning from a wedding.
In 2002, 373 people died when a fire ripped through a crowded train south of the capital.
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