Due to a points failure between Doncaster and Wakefield Westgate, some lines are blocked.
Northern said train services running through these stations will be cancelled or delayed by up to 60 minutes.
Disruption is expected until at least 1pm today.
Network rail engineers are on site working to rectify the fault, Northern said.
Services between Doncaster and Leeds are unable to run at this time.
Services from Sheffield to Leeds will be diverted between Meadowhall and Wakefield Westgate.
Services from Leeds to Sheffield are unaffected at this time.
Customers at Sheffield and Meadowhall requiring Wakefield and Leeds can travel on Sheffield to Leeds via Barnsley services.
Northern tickets will be accepted on LNER services between York and Doncaster to connect with Northern services that run between York and Leeds.
Road transport has been requested between Wakefield Westgate and Doncaster and Swinton and Wakefield Westgate.
If you've been delayed by 15 minutes or more, hold on to your tickets and claim compensation by visiting www.northernrailway.co.uk/delayrepay