The train, which was transporting grain, crashed in Ecatepec, a large municipality that forms part of the urban sprawl extending from the capital.
After the train ran off the tracks shortly before 6am local time, one of its cars careened into a residential area, killing five people, the Communications and Transportation Ministry said in a statement.
The train belonged to Kansas City Southern’s Mexican unit, the ministry said.
In a statement, railroad and terminals operator Ferrovalle, which is partially owned by Kansas City Southern de México, lamented the accident, the causes of which were still unknown.
Ferrovalle said it and Kansas City Southern de México would work with authorities to find out what happened and prevent it from occurring again.
The Mexican regulator for railway transport will investigate the accident, the ministry said.
“The government of Ecatepec sends its deepest condolences to the families of the victims and reiterates its support in this difficult moment,” Mayor Indalecio Ríos wrote on Twitter.