Services between Wakefield and Leeds have been cancelled after a train broke down on the lines.
Northern said there was "no estimate" for when services would return to normal.
Services between Leeds, Doncaster, Sheffield and Knottingley, as well as Wakefield Kirkgate, Streethouse, Featherstone and Pontefract are among those affected.
In a statement, Northern Rail said: "Due to a broken down LNER train between Leeds and Wakefield Westgate, services out of Leeds towards Doncaster, Sheffield and Knottingley are currently being disrupted.
"A line blockage is currently in place and a rescue unit is now en-route from Doncaster to bring the train back into Leeds. At present, there is no estimate for when services will return to normal."
Disruption was first reported shortly after 1pm today (Tuesday, January 7), though Northern had initially said they hopes to resume normal services by 2.30pm.
Commuters face delays and cancellations on services this afternoon and are advised to check the latest travel advice from their train operator before travelling.
People who face delays of more than 15 minutes are advised to visit northernrailway.co.uk/delayrepay.
Update, 4.14pm: The affected train has now been moved and all lines are reopen. However, National Rail have said that disruption is likely to continue until at least 5pm.