Translink has said there will be a bus substitution service between Lisburn and Portadown in both directions due to the signalling failure.
The Enterprise services are operating from Belfast Central and calling at Moira and Luran as well as normal stops.
Passengers are warned to expect delays.
However a number have voiced anger at the length of the delays and the lack of communication.
A Translink spokesperson said: “A bus substitution in currently operating between Lisburn and Portadown in both directions until further notice, due to a signalling failure.
“Rail tickets are being be accepted on scheduled bus services between these two points.
“Enterprise services are operating from Belfast Central and calling at Moira and Lurgan in addition to the normal scheduled timetabled stops, however passengers should expect some delays.
“We have engineers currently on site and we are working hard to resolve this issue as quickly as we can.
“We apologise for any inconvenience caused.”