The collision took place after a train from the Egyptian capital Cairo collided with another train coming from Port Said in Khorshid area, Ministry of Health officials said.
"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 victims could increase.
The Health ministry is yet to announce the final toll. At least 36 people have been killed and 123 injured in the accident.
Train accidents are common in Egypt. In 2016, a train derailed in the south of Cairo, killing five people, and injuring 27 people in the al-Ayat area.