The train caught fire near Dunton Green, Kent, blocking both lines between Sevenoaks and Orpington.
In a series of tweets, Network Rail has confirmed that nobody has been injured and the fire has now been put out.
Network Rail engineers will now move the damaged tamper, a machine which restores the level of the track, to check for damage to the track and assess what repairs might be needed.
Network Rail estimates that it could take most of this morning to clear.
A Network Rail Kent and Sussex tweet added: We don’t know yet what caused the fire but are working with Kent Fire Rescue who are investigating. We have lots of people on site right now working to get passengers moving again and that’s our priority. We’re sorry for the disruption this has caused.