A cut cable caused signalling problems on the railway lines resulting in commuter chaos at Lurgan and Portadown.
Translink said a communications cable had been cut.
Although bus substitutions have been put in place, many passengers have vented anger on social media due to the lengthy delays and lack of communication.
The Enterprise train is now running from Belfast Central Station, making extra stops at Lurgan and Moira.
Translink apologised for any inconvenience.
Ciaran Doherty of Translink said: “We were doing some scheduled maintenance works on the line into the night and unfortunately we managed to cut one of the communications cables on the line which caused the problem,” he said.
He said they had been “working hard all day to ensure the problem does not roll into this evening”.
“What I can say is that this evening all services are planned to be leaving as normal out of Belfast on the Portadown line,” he added.
“There is a possibility of further delays beyond Lisburn but what we are trying to do is to work hard to make sure they don’t ensue.”
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.”
Meanwhile, motorists also faced delays on the M1, as traffic signals at the junction nine off-slip at Moira were not working.