Carriages derailed and overturned when two trains collided near the city of Tahta in Sohag province on Friday.
Officials originally put the death toll at 32, but later revised that figure.
An investigation has been launched into the crash, with President Abdul Fattah al-Sisi pledging tough punishment for those 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.
The country's railway authority said emergency brakes were activated on the train in front by "unknown individuals", causing the train behind to crash into it.
Health Minister Hala Zayed revised down the official death toll on Saturday, saying some unconscious victims had been wrongly pronounced dead at the scene.
The incident happened about 365km (227 miles) south of the capital Cairo.
One of the trains was travelling between the southern city of Luxor and the Mediterranean port of Alexandria, while the other was travelling between the capital Cairo and the city of Aswan in southern Egypt.
More than 70 ambulances were sent to the crash site to take the injured to hospitals.
Photos from the scene showed carriages overturned near a channel of water.
"People are dead, we can't even save the ones who are alive," a man at the scene told Reuters news agency on Friday.
Prime Minister Mostafa Madbouly visited the site of the crash, promising financial compensation to the victims' families.
Mr Madbouly said the government would continue to upgrade railway projects to prevent similar deadly accidents, Egypt's Ahramonline website reports.
Egypt has seen frequent accidents on its railway system due in part to poor maintenance and lack of investment.
One of the deadliest train disasters occurred in 2002 when 373 people died after a fire broke out on a train travelling south of Cairo.