Trains to and from Leeds Station are being cancelled or delayed due to a points failure at Leeds Station.
Northern Rail has now warned passengers to "plan carefully" as disruption is set to last for the rest of the day.
Last minute 'late-notice' delays are also warned to be likely.
Some services are cancelled completely until further notice.
These include the Huddersfield to Leeds line which calls at key commuter stations including Brighouse, Bradford Interchange, New Pudsey and Bramley.
The Leeds to Knottingley line is also cancelled today, meanings passengers travelling to Wakefield stations, Featherstone and Pontefract stations will have to make alternative arrangements.
Services via Castleford are unaffected.
Northern Rail said that there is no estimated time when the repair work will be completed and that the evening peak hour will be "particularly difficult."
A spokesman for Northern said: “The points failure means we are unable to run all our services and we’re calling on our customers to plan carefully for the rest of Tuesday. Colleagues from Network Rail are on-scene and working to fix the points, but we have no estimate for when this will be completed.
“The evening peak is going to be particularly difficult, but we are working with Network Rail, other operators and bus providers to try to keep people on the move.”
Services between Leeds and Manchester Victoria will call additionally at Low Moor
Buses will operate between Halifax and Huddersfield (via Brighouse) on the hour, every hour.
They will run until 11pm and there will also be buses in the opposite direction running until 9.53pm.
A one-off bus service, at 10.50pm will operate between Huddersfield and Leeds.
Ticket acceptance is in place for LNER services between Leeds and Wakefield Westgate.
Trains are able to run from Huddersfield to Leeds via Dewsbury and Manchester to Leeds in all directions.
Passengers at Brighouse can use the service to and from Manchester Victoria and change for alternative trains at Mirfield, Dewsbury and Sowerby Bridge.