Railroad spokesperson Amy Williams told local news station KSHB that the incident occurred at about 11.10pm in Rushville, Buchanan County.
No-one was injured in the nine-car derailment.
The 134-car train with two locomotives on board was traveling from Rushville to Kansas City, though Williams said the destination was not the final one for the load.
BNSF, which could not confirm when the line would reopen, is investigating the cause of the incident.
Earlier this month, railroad officials said regional coal train traffic was back to normal after a train from the Powder River Basin derailed in South Dakota.
Thirty-seven cars of the 123-car BNSF train left the tracks in Dewey, Custer County, on its way from Wyoming to Nebraska, though no injuries were reported.