Luis Felipe Puente, the national civil protection coordinator, confirmed the toll on Twitter, adding that 16 of the injured were in "serious" condition following the incident in the state of Tabasco.
The train, known as "The Beast," carries Mexican and Central American migrants with many sitting on top of the cars after paying smugglers upwards of USD 100 for the right to travel.
The train derailed on a stretch of tracks alongside a river and the site of the accident is only accessible by boat, a public security official from the municipality of Huimanguillo told AFP.