Northern Rail said that all routes between the two destinations were blocked and that Network Rail staff were on site assessing the situation.
It is not clear exactly where the problem is on the route.
A spokesman said: "Due to a fault with the signalling system between Leeds and Doncaster, all lines are blocked.
"Train services running through these stations may be cancelled, delayed or diverted between Leeds and Halifax.
"Some stations between Leeds and Doncaster will not be served.
"Network Rail staff are currently on site working to resolve the issue."