National Rail has warned passengers to expect disruption to services between the two stations for the rest of the day.
Journey times are being extended by up to 90 minutes as a result.
It is affecting services operated by Virgin Trains East Coast, Hull Trains, Transpennine Express and Cross Country.
Virgin Trains has made a separate warning about damaged overhead wires, which also appears to be affecting its services.
Earlier, its London-bound services were also having to run at reduced speeds between Leeds and Wakefield due to a signalling problem.
Virgin Trains has advised customers not to travel at all today if possible and promised that tickets would be valid for travel tomorrow.
Virgin Trains East Coast customers may use TransPennine Express services between York and Leeds, East Midlands Trains services via any reasonable route, CrossCountry services via any reasonable route, and Virgin Trains West Coast services between Scotland and York.
Hull Trains customers may use CrossCountry services via any reasonable route, Virgin Trains East Coast services via any reasonable route, and Northern services via any reasonable route.
TransPennine Express customers may use Northern services between Leeds and Manchester Victoria, CrossCountry services via any reasonable route and Virgin Trains East Coast via any reasonable route.
CrossCountry customers may use Northern services between Sheffield and Doncaster, and TransPennine Express services between Sheffield and Doncaster.