The ministry noted that 19 of the injured have been treated and discharged from the hospital, while two others remain under medical care, Xinhua news agency reported.
"One fatality was transferred to Minya General Hospital, and rescue teams are still working at the accident site," the ministry added.
Earlier, Egypt's railway authority explained that a locomotive collided with the rear of a train travelling from Aswan to Cairo, causing the power car and a passenger car to detach and fall into a nearby canal.
Transport Minister Kamel al-Wazir has ordered a committee to investigate the technical causes of the crash, according to a railway authority statement.
Egypt's state-run Ahram Online later reported that the death toll has risen to two, although the Health Ministry did not confirm the update.
Eyewitnesses told Xinhua that local residents and fishermen from Minya assisted in rescue efforts at the Ibrahimiyah Canal in Maqusah village, where the accident occurred.
Train traffic resumed after hours of disruption caused by the collision, the Minya provincial government said in a statement.