Authorities said the death toll could rise after the train known as "The Beast," which carries Central American migrants who pay smugglers to sit atop freight cars, careened off the track near a river in Tabasco state.
A Tabasco public security spokesman told AFP the death toll had risen from five to six at midday and "the search (for survivors) continues."
Tabasco civil protection director Cesar Burelo told Milenio television that 16 people were taken to the regional hospital of Las Choapas in the neighboring state of Veracruz, which is 25 minutes away by boat.
"The Beast" carries Mexican and Central American migrants who pay smugglers upwards of USD 100 for the right to travel from stations near Guatemala to the north of Mexico.
More From This Section
Eight of the train's 12 freight cars overturned at around 3:00 am, state officials said. Rescuers used hydraulic tools to cut through the metal to find survivors.
Burelo said cranes will be needed to lift the wagons, which could lead to discoveries of more fatalities.
He told Formato 21 radio that "we could possibly have more dead."
Local officials said the accident took place far from any road in the municipality of Huimanguillo, near the state of Veracruz, and that the site was only accessible by air or boat.
A photo broadcast by Milenio television showed freight cars lying on their side with the wheels detached from the bottom. The tracks are seen in a wooded area and covered with plants.
Huimanguillo civil protection and security officials told AFP that between 250 and 300 migrants were aboard the train.
At least one of dead is from Honduras, according to Tabasco civil protection.