An al Jazeera reporter quoted a railway department official as saying the accident was caused by a "technical fault".
Sudan has an extensive rail network, much of it built by Britain, the former colonial power, but most of the rolling stock is old.
The crash occurred two days after a plane crash near the southern town of Rumbek that killed at least 23 people, including Dominic Dim, Southern Sudan's minister of defence.
Justin Yak, a presidential adviser for local government affairs, and his wife were also among the dead.
The plane crash was blamed on engine failure.