The collision occurred when a train from the Egyptian capital Cairo collided with another train coming from Port Said in Khorshid area, Health ministry officials said.
The transport ministry said that the train coming from Cairo to Alexandria crashed into the back of the train coming from Port Said to Alexandria, which was stationary at Khorsid station when the collision occurred which left at least 41 dead and 179 injured, ahramonline reported quoting a Health ministry statement.
Egypt's prosecutor-general Nabil Sadiq has ordered an urgent investigation into the collision to find out the reason behind the crash.
President El-Sisi has expressed his condolences to the victims and ordered government bodies to follow up on developments from the deadly collision and identify the cause of the accident.
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"The rescue team is currently searching for survivals while ambulances are transferring the injured to nearby hospitals," said Magdy Hegazi, undersecretary at the Health ministry.
Earlier, Health Minister advisor Sherif Wadie said that the number of casualties could increase.
The cause of the crash is not yet known.
The Health ministry is yet to announce the final toll.
Train accidents are common in Egypt. In 2016, a train derailed in south of Cairo, killing five people, and injuring 27 people in the al-Ayat area.
Another train derailment in Badr Rashin in Giza killed at least 19 people in 2013.
In 2012, a collision between a train and school bus on a rail crossing in the town of Manaflut in Upper Egypt killed 51 people, mostly children.