National Rail said the disruption has caused lines in both directions to be blocked between Doncaster and Wakefield Westgate railway stations.
It has warned that London North Eastern Railway and Northern trains between Swinton, Doncaster and Wakefield are likely to be cancelled, delayed or revised as a result.
The delays are expected until at least 2pm today (Tuesday).
It comes after rail commuters heading towards West Yorkshire yesterday also faced heavy rush hour delays, following a signalling fault in Wakefield.