On Wednesday night, the incident took place on the West Coast Main Line between Penrith and Oxenholme Lake District.
There is very little rail service operating on the lines that are still open while some routes are blocked.
Train companies TransPennine Express and Avanti West Coast issued the warning, advising passengers not to attempt to use their services on Thursday for journeys between Preston and Scotland.
Ticket holders have the option to travel with different operators or postpone trips until Friday.
In addition to offering its condolences to the impacted passengers, Network Rail warned that there will be service disruptions for the remainder of the day.
It stated that expert repair crews were on the scene and were attempting to secure the railway as quickly as possible.
“We are working hard to move a partially derailed freight train near Shap, between Oxenholme and Penrith on the West Coast Main Line,” a spokesperson told News.
“We sincerely apologize to travelers whose travel plans have been inconvenienced while we endeavor to promptly and safely restart the line.
“Please check before you travel if travelling north of Preston.”
