Two carriages were derailed and overturned when two passenger trains collided in the province of Sohag.
Emergency brakes were activated on the train in front by “unknown individuals”, causing the train behind to crash into it, the authority said.
Officials are investigating the cause of the crash.
Egyptian President Abdel Fattah al-Sisi said there would be serious consequences for anyone found responsible.
“Anyone who caused this painful accident through negligence or corruption, or anything similar, must receive a deterrent punishment without exception or delay,” he tweeted.
Photos from the scene show carriages overturned near a channel of water.
In a statement, the health ministry said that at least 108 people were injured in addition to the fatalities.
“We need an official to come to see what has happened. They can’t remove the people from underneath the trains,” a man at the scene told Reuters news agency, adding that a crane was needed to help with rescue efforts.
“People are dead, and we can’t even save the ones who are alive.”
Prime Minister Mostafa Madbouly is travelling to the crash site with the ministers, state media reported.
Egypt has seen frequent accidents on its railway system due to poor maintenance and lack of investment.
One of the deadliest train disasters occurred in 2002 when 373 people died when a fire broke out in a carriage travelling south of Cairo.