Trains between Giza and the Upper Egypt region were suspended as cranes were dispatched to remove the wrecked trains.
The collision occurred in the area between Kafr Ammar and Al-Raqqa stations in Al-Ayyat, close to where Egypt’s deadliest train tragedy occurred in February 2002, when a fire engulfed a passenger train travelling from Cairo to Luxor.
The train continued for around nine kilometres (5.6 miles) before coming to a halt.
In that incident, more than 370 people were officially reported killed, although some estimates put the toll considerably higher.
Two further crashes in the area in 2009 killed dozens more.
There were calls in Egypt on Sunday for the transport minister to resign over the latest deadly rail disaster.
