A train collision near Alexandria on Friday left at least 41 dead and 179 injured, a statement from the health ministry read.
One of the trains was travelling from Cairo to Alexandria, and the other from Port Said to Alexandria.
The transport ministry said in an official statement 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 Khorshid station when the collision occurred.
The driver of the Cairo-Alexandria train has surrendered himself to police and has been transferred to El-Raml police station in Alexandria pending investigations, according to Al-Ahram Arabic website.
Khorshid station is on the Cairo-Alexandria line southeast of Alexandria on the Mediterranean.
Egypt's prosecutor-general, Nabil Sadiq, has ordered an urgent investigation into the collision.
Speaking on Friday evening, President El-Sisi expressed his condolences to the victims and ordered government bodies to follow up on developments from the deadly collision, and to form investigative work teams in order to identify the reasons behind the accident and hold those responsible to account.
Health ministry spokesman Khaled Megahed said that the dead were transferred to Koum El-Dekka morgue, while injured passengers are mainly at El-Mery, El-Gomhoria, Ras El-Tin, and Mostafa Kamel hospitals.
Social Solidarity Minister Ghada Wali has said that the ministry will provide EGP 50,000 in compensation to the families of those killed.
Compensation for those injured will be determined on a case-by-case basis, Al-Ahram reported.
The American embassy in Cairo wrote on Twitter that "Our thoughts & prayers w/ families of those killed & injured in today's train crash. We stand with the Egyptian people in this hard time.”
A number of other foreign missions in Cairo have also expressed their condolences following the deadly accident, including the Ukrainian, British and German embassies.
El-Sisi has also received condolences from a number of Arab countries, including Kuwaiti Emir Sheikh Sabah Ahmed El-Gaber Al-Sabah, Jordanian King Abdulluh, and Palestinian President Mahmoud Abbas, according to MENA.
Mass-casualty train accidents in Egypt are not unknown.
A train derailment in Badrashin 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 Manfalut in Upper Egypt killed 51 people, mostly children.