The collision occurred in the province of Minya, 270 kilometers (about 168 miles) south of Cairo, the railway authority said in a statement, adding that two railway carriages fell into an adjacent watercourse.
The cause of the crash was being investigated, according to the statement. Footage aired by local media showed the two carriages partially submerged in the watercourse.
The Health Ministry said in a separate statement at least 20 people were taken to hospitals.
Train derailments and crashes are common in Egypt, where an aging railway system has been plagued by mismanagement. In September, two passenger trains collided in a Nile Delta city, killing at least three people.
In recent years, the government announced initiatives to improve its railways. President Abdel Fattah el-Sissi said in 2018 some 250 billion Egyptian pounds, or $8.13 billion, would be needed to properly overhaul the neglected rail network.